diff --git a/404.html b/404.html index 2aca358d..49a42669 100644 --- a/404.html +++ b/404.html @@ -4,130 +4,83 @@ - + Page not found (404) • MultiAssayExperiment - - - - - - - + + + + + - - - -
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- - + diff --git a/articles/MultiAssayExperiment.html b/articles/MultiAssayExperiment.html index 9b6142f6..aef78e56 100644 --- a/articles/MultiAssayExperiment.html +++ b/articles/MultiAssayExperiment.html @@ -4,108 +4,71 @@ - + MultiAssayExperiment: The Integrative Bioconductor Container • MultiAssayExperiment - - - - - - - - + + + + + - - + + Skip to contents -
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+

Citing MultiAssayExperiment +

+

Without your citations our free and open-source software would not be +possible. Please cite MultiAssayExperiment as shown in the +References section (Ramos et al. (2017)). You may also refer to the +Cancer Research publication at the AACR Journals link here.

+
+

A Brief Description

MultiAssayExperiment offers a data structure for @@ -1510,12 +1481,13 @@

Subsetting rows (features) by ## [1] Affy: SummarizedExperiment with 0 rows and 4 columns ## [2] Methyl 450k: matrix with 0 rows and 5 columns ## [3] Mirna: matrix with 0 rows and 3 columns -## [4] CNV gistic: RangedSummarizedExperiment with 0 rows and 4 columns +## [4] CNV gistic: RangedSummarizedExperiment with 1 rows and 4 columns
 rowRanges(subsetted[[4]])
-
## GRanges object with 0 ranges and 1 metadata column:
-##    seqnames    ranges strand |  feature_id
-##       <Rle> <IRanges>  <Rle> | <character>
+
## GRanges object with 1 range and 1 metadata column:
+##     seqnames        ranges strand |  feature_id
+##        <Rle>     <IRanges>  <Rle> | <character>
+##   a     chr1 317182-317281      - |     ID\\001
 ##   -------
 ##   seqinfo: 2 sequences from an unspecified genome; no seqlengths

Square bracket subsetting can still be used here, but passing on @@ -1816,10 +1788,10 @@

## DataFrame with 4 rows and 3 columns
 ##          slope53         sex       age
 ##        <numeric> <character> <integer>
-## array1 -0.873747           M        38
-## array2  0.135897           F        39
-## array3  0.766453           F        41
-## array4 -2.020816           M        40
+## array1 0.106685 M 38 +## array2 -0.587014 F 39 +## array3 -0.327854 F 41 +## array4 -0.085361 M 40

 class(affex)
## [1] "SummarizedExperiment"
@@ -1843,19 +1815,19 @@ 

## harmonizing input:
 ##   removing 7 sampleMap rows not in names(experiments)
## DataFrame with 18 rows and 5 columns
-##           assay     primary         rowname     colname     value
-##     <character> <character>     <character> <character> <integer>
-## 1          Affy        Jack ENST00000294241      array1       101
-## 2          Affy        Jack ENST00000355076      array1       102
-## 3          Affy        Jill ENST00000294241      array2       103
-## 4          Affy        Jill ENST00000355076      array2       104
-## 5          Affy     Barbara ENST00000294241      array3       105
-## ...         ...         ...             ...         ...       ...
-## 14  Methyl 450k        Jill ENST00000383706     methyl3         6
-## 15  Methyl 450k     Barbara ENST00000355076     methyl4         7
-## 16  Methyl 450k     Barbara ENST00000383706     methyl4         8
-## 17  Methyl 450k         Bob ENST00000355076     methyl5         9
-## 18  Methyl 450k         Bob ENST00000383706     methyl5        10
+## assay primary rowname colname value +## <character> <character> <character> <factor> <integer> +## 1 Affy Jack ENST00000294241 array1 101 +## 2 Affy Jack ENST00000355076 array1 102 +## 3 Affy Jill ENST00000294241 array2 103 +## 4 Affy Jill ENST00000355076 array2 104 +## 5 Affy Barbara ENST00000294241 array3 105 +## ... ... ... ... ... ... +## 14 Methyl 450k Jill ENST00000383706 methyl3 6 +## 15 Methyl 450k Barbara ENST00000355076 methyl4 7 +## 16 Methyl 450k Barbara ENST00000383706 methyl4 8 +## 17 Methyl 450k Bob ENST00000355076 methyl5 9 +## 18 Methyl 450k Bob ENST00000383706 methyl5 10

This is especially useful for performing regression against patient or sample data from colData using the pDataCols argument:

@@ -1865,19 +1837,19 @@

## harmonizing input:
 ##   removing 7 sampleMap rows not in names(experiments)
## DataFrame with 18 rows and 6 columns
-##           assay     primary         rowname     colname     value       age
-##     <character> <character>     <character> <character> <integer> <integer>
-## 1          Affy        Jack ENST00000294241      array1       101        38
-## 2          Affy        Jack ENST00000355076      array1       102        38
-## 3          Affy        Jill ENST00000294241      array2       103        39
-## 4          Affy        Jill ENST00000355076      array2       104        39
-## 5          Affy     Barbara ENST00000294241      array3       105        41
-## ...         ...         ...             ...         ...       ...       ...
-## 14  Methyl 450k        Jill ENST00000383706     methyl3         6        39
-## 15  Methyl 450k     Barbara ENST00000355076     methyl4         7        41
-## 16  Methyl 450k     Barbara ENST00000383706     methyl4         8        41
-## 17  Methyl 450k         Bob ENST00000355076     methyl5         9        40
-## 18  Methyl 450k         Bob ENST00000383706     methyl5        10        40
+## assay primary rowname colname value age +## <character> <character> <character> <factor> <integer> <integer> +## 1 Affy Jack ENST00000294241 array1 101 38 +## 2 Affy Jack ENST00000355076 array1 102 38 +## 3 Affy Jill ENST00000294241 array2 103 39 +## 4 Affy Jill ENST00000355076 array2 104 39 +## 5 Affy Barbara ENST00000294241 array3 105 41 +## ... ... ... ... ... ... ... +## 14 Methyl 450k Jill ENST00000383706 methyl3 6 39 +## 15 Methyl 450k Barbara ENST00000355076 methyl4 7 41 +## 16 Methyl 450k Barbara ENST00000383706 methyl4 8 41 +## 17 Methyl 450k Bob ENST00000355076 methyl5 9 40 +## 18 Methyl 450k Bob ENST00000383706 methyl5 10 40

The “wide” format is useful for calculating correlations or performing regression against different genomic features. Wide format is in general not possible with replicate measurements, so we demonstrate @@ -1987,7 +1959,7 @@

Requirements for su

Application Programming Interface (API)

For more information on the formal API of -MultiAssayExperiment, please see the API +MultiAssayExperiment, please see the API wiki document on GitHub. An API package is available for download on GitHub via install("waldronlab/MultiAssayShiny"). It provides visual exploration of available methods in @@ -2017,36 +1989,13 @@

Methods for MultiAssayExperiment## see '?methods' for accessing help and source code

-

Citing MultiAssayExperiment -

-

We are excited to announce the official citation for -MultiAssayExperiment in Cancer Research.

-
-citation("MultiAssayExperiment")
-
## To cite MultiAssayExperiment in publications use:
-## 
-##   Marcel Ramos et al. Software For The Integration Of Multiomics
-##   Experiments In Bioconductor. Cancer Research, 2017 November 1;
-##   77(21); e39-42. DOI: 10.1158/0008-5472.CAN-17-0344
-## 
-## A BibTeX entry for LaTeX users is
-## 
-##   @Article{,
-##     title = {Software For The Integration Of Multi-Omics Experiments In Bioconductor},
-##     author = {Marcel Ramos and Lucas Schiffer and Angela Re and Rimsha Azhar and Azfar Basunia and Carmen Rodriguez Cabrera and Tiffany Chan and Philip Chapman and Sean Davis and David Gomez-Cabrero and Aedin C. Culhane and Benjamin Haibe-Kains and Kasper Hansen and Hanish Kodali and Marie Stephie Louis and Arvind Singh Mer and Markus Reister and Martin Morgan and Vincent Carey and Levi Waldron},
-##     journal = {Cancer Research},
-##     year = {2017},
-##     volume = {77(21); e39-42},
-##   }
-
-

sessionInfo()

-
+
-
## R version 4.3.2 (2023-10-31)
-## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 22.04.3 LTS
+
## R version 4.4.1 (2024-06-14)
+## Platform: x86_64-pc-linux-gnu
+## Running under: Ubuntu 22.04.4 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -2068,67 +2017,71 @@ 

sessionInfo()## [8] base ## ## other attached packages: -## [1] RaggedExperiment_1.26.0 MultiAssayExperiment_1.28.0 -## [3] SummarizedExperiment_1.32.0 Biobase_2.62.0 -## [5] GenomicRanges_1.54.1 GenomeInfoDb_1.38.5 -## [7] IRanges_2.36.0 S4Vectors_0.40.2 -## [9] BiocGenerics_0.48.1 MatrixGenerics_1.14.0 -## [11] matrixStats_1.2.0 BiocStyle_2.30.0 +## [1] RaggedExperiment_1.28.1 MultiAssayExperiment_1.30.3 +## [3] SummarizedExperiment_1.34.0 Biobase_2.64.0 +## [5] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 +## [7] IRanges_2.38.1 S4Vectors_0.42.1 +## [9] BiocGenerics_0.50.0 MatrixGenerics_1.16.0 +## [11] matrixStats_1.3.0 BiocStyle_2.32.1 ## ## loaded via a namespace (and not attached): -## [1] xfun_0.41 bslib_0.6.1 lattice_0.22-5 -## [4] vctrs_0.6.5 tools_4.3.2 bitops_1.0-7 +## [1] xfun_0.46 bslib_0.8.0 htmlwidgets_1.6.4 +## [4] lattice_0.22-6 vctrs_0.6.5 tools_4.4.1 ## [7] generics_0.1.3 tibble_3.2.1 fansi_1.0.6 -## [10] highr_0.10 pkgconfig_2.0.3 BiocBaseUtils_1.4.0 -## [13] Matrix_1.6-5 desc_1.4.3 lifecycle_1.0.4 -## [16] GenomeInfoDbData_1.2.11 compiler_4.3.2 stringr_1.5.1 -## [19] textshaping_0.3.7 htmltools_0.5.7 sass_0.4.8 -## [22] RCurl_1.98-1.14 yaml_2.3.8 pkgdown_2.0.7 -## [25] pillar_1.9.0 crayon_1.5.2 jquerylib_0.1.4 -## [28] tidyr_1.3.0 DelayedArray_0.28.0 cachem_1.0.8 -## [31] abind_1.4-5 tidyselect_1.2.0 digest_0.6.34 -## [34] stringi_1.8.3 dplyr_1.1.4 purrr_1.0.2 -## [37] bookdown_0.37 fastmap_1.1.1 grid_4.3.2 -## [40] cli_3.6.2 SparseArray_1.2.3 magrittr_2.0.3 -## [43] S4Arrays_1.2.0 utf8_1.2.4 withr_3.0.0 -## [46] rmarkdown_2.25 XVector_0.42.0 ragg_1.2.7 -## [49] memoise_2.0.1 evaluate_0.23 knitr_1.45 -## [52] rlang_1.1.3 glue_1.7.0 BiocManager_1.30.22 -## [55] jsonlite_1.8.8 R6_2.5.1 systemfonts_1.0.5 -## [58] fs_1.6.3 zlibbioc_1.48.0

+## [10] highr_0.11 pkgconfig_2.0.3 BiocBaseUtils_1.6.0 +## [13] Matrix_1.7-0 desc_1.4.3 lifecycle_1.0.4 +## [16] GenomeInfoDbData_1.2.12 compiler_4.4.1 stringr_1.5.1 +## [19] textshaping_0.4.0 htmltools_0.5.8.1 sass_0.4.9 +## [22] yaml_2.3.10 pkgdown_2.1.0 pillar_1.9.0 +## [25] crayon_1.5.3 jquerylib_0.1.4 tidyr_1.3.1 +## [28] DelayedArray_0.30.1 cachem_1.1.0 abind_1.4-5 +## [31] tidyselect_1.2.1 digest_0.6.36 stringi_1.8.4 +## [34] purrr_1.0.2 dplyr_1.1.4 reshape2_1.4.4 +## [37] bookdown_0.40 fastmap_1.2.0 grid_4.4.1 +## [40] cli_3.6.3 SparseArray_1.4.8 magrittr_2.0.3 +## [43] S4Arrays_1.4.1 utf8_1.2.4 withr_3.0.1 +## [46] UCSC.utils_1.0.0 rmarkdown_2.27 XVector_0.44.0 +## [49] httr_1.4.7 ragg_1.3.2 evaluate_0.24.0 +## [52] knitr_1.48 rlang_1.1.4 Rcpp_1.0.13 +## [55] glue_1.7.0 BiocManager_1.30.23 jsonlite_1.8.8 +## [58] R6_2.5.1 plyr_1.8.9 systemfonts_1.1.0 +## [61] fs_1.6.4 zlibbioc_1.50.0

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## <50000 x 20> HDF5Matrix object of type "double":
-##             SampleID1   SampleID2   SampleID3 ...  SampleID19  SampleID20
-##     GENE1  -0.3875569  -0.9245979  -0.4860061   .  0.88458768 -1.61563992
-##     GENE2  -0.2644658   0.3048011  -0.9763176   .  0.62873303  0.11844208
-##     GENE3  -1.0037401  -0.6172604   0.2084938   . -1.03015889 -1.61369308
-##     GENE4  -1.1815745  -1.5556907   0.6032805   . -1.30802616  0.07655268
-##     GENE5  -2.9104018   2.4867479   3.2304527   . -0.39682861  2.10575923
-##       ...           .           .           .   .           .           .
-## GENE49996  0.08974065  0.65075160 -0.07995008   .   0.5827023   0.1526415
-## GENE49997  0.70751975  1.37734494 -2.00313995   .   0.6547790   1.4318531
-## GENE49998  0.74370046 -0.04946058 -0.31213299   .  -2.4141129  -1.5732835
-## GENE49999 -2.61420539 -1.09089104  0.91170686   .   1.0285334  -0.3192227
-## GENE50000  0.42807965 -0.71061527  0.39352464   .   0.2416611  -0.7500389
+## SampleID1 SampleID2 SampleID3 ... SampleID19 SampleID20 +## GENE1 -1.400043517 1.431663588 -1.336606503 . -2.307774531 -2.293199815 +## GENE2 0.255317055 0.171127984 0.089914742 . 0.614199996 -0.335822358 +## GENE3 -2.437263611 2.312015552 0.379995935 . -0.733181166 0.083092829 +## GENE4 -0.005571287 -0.057850207 -0.056034294 . 0.818604632 0.106635015 +## GENE5 0.621552721 -0.975709562 0.700863028 . 0.005259257 1.643080357 +## ... . . . . . . +## GENE49996 0.2027090 0.4424774 0.6336781 . -0.47392601 0.28854415 +## GENE49997 1.2847634 1.2558989 1.2587418 . -2.52268507 -1.77342923 +## GENE49998 0.2648680 1.3883708 -0.3003243 . -1.76756368 0.76883529 +## GENE49999 1.4098422 0.2065422 -0.4955832 . 1.59338432 -0.05131006 +## GENE50000 -0.7546331 0.6750468 0.1188484 . -1.25230132 0.30771323

To see the file structure we use h5ls:

 h5ls(testh5)
@@ -218,18 +181,18 @@

Importing HDF5 files
 newDelayedMatrix

## <50000 x 20> HDF5Matrix object of type "double":
-##             SampleID1   SampleID2   SampleID3 ...  SampleID19  SampleID20
-##     GENE1  -0.3875569  -0.9245979  -0.4860061   .  0.88458768 -1.61563992
-##     GENE2  -0.2644658   0.3048011  -0.9763176   .  0.62873303  0.11844208
-##     GENE3  -1.0037401  -0.6172604   0.2084938   . -1.03015889 -1.61369308
-##     GENE4  -1.1815745  -1.5556907   0.6032805   . -1.30802616  0.07655268
-##     GENE5  -2.9104018   2.4867479   3.2304527   . -0.39682861  2.10575923
-##       ...           .           .           .   .           .           .
-## GENE49996  0.08974065  0.65075160 -0.07995008   .   0.5827023   0.1526415
-## GENE49997  0.70751975  1.37734494 -2.00313995   .   0.6547790   1.4318531
-## GENE49998  0.74370046 -0.04946058 -0.31213299   .  -2.4141129  -1.5732835
-## GENE49999 -2.61420539 -1.09089104  0.91170686   .   1.0285334  -0.3192227
-## GENE50000  0.42807965 -0.71061527  0.39352464   .   0.2416611  -0.7500389
+## SampleID1 SampleID2 SampleID3 ... SampleID19 SampleID20 +## GENE1 -1.400043517 1.431663588 -1.336606503 . -2.307774531 -2.293199815 +## GENE2 0.255317055 0.171127984 0.089914742 . 0.614199996 -0.335822358 +## GENE3 -2.437263611 2.312015552 0.379995935 . -0.733181166 0.083092829 +## GENE4 -0.005571287 -0.057850207 -0.056034294 . 0.818604632 0.106635015 +## GENE5 0.621552721 -0.975709562 0.700863028 . 0.005259257 1.643080357 +## ... . . . . . . +## GENE49996 0.2027090 0.4424774 0.6336781 . -0.47392601 0.28854415 +## GENE49997 1.2847634 1.2558989 1.2587418 . -2.52268507 -1.77342923 +## GENE49998 0.2648680 1.3883708 -0.3003243 . -1.76756368 0.76883529 +## GENE49999 1.4098422 0.2065422 -0.4955832 . 1.59338432 -0.05131006 +## GENE50000 -0.7546331 0.6750468 0.1188484 . -1.25230132 0.30771323
## <50000 x 20> DelayedMatrix object of type "double":
-##             SampleID1   SampleID2   SampleID3 ...  SampleID19  SampleID20
-##     GENE1  -0.3875569  -0.9245979  -0.4860061   .  0.88458768 -1.61563992
-##     GENE2  -0.2644658   0.3048011  -0.9763176   .  0.62873303  0.11844208
-##     GENE3  -1.0037401  -0.6172604   0.2084938   . -1.03015889 -1.61369308
-##     GENE4  -1.1815745  -1.5556907   0.6032805   . -1.30802616  0.07655268
-##     GENE5  -2.9104018   2.4867479   3.2304527   . -0.39682861  2.10575923
-##       ...           .           .           .   .           .           .
-## GENE49996  0.08974065  0.65075160 -0.07995008   .   0.5827023   0.1526415
-## GENE49997  0.70751975  1.37734494 -2.00313995   .   0.6547790   1.4318531
-## GENE49998  0.74370046 -0.04946058 -0.31213299   .  -2.4141129  -1.5732835
-## GENE49999 -2.61420539 -1.09089104  0.91170686   .   1.0285334  -0.3192227
-## GENE50000  0.42807965 -0.71061527  0.39352464   .   0.2416611  -0.7500389
+## SampleID1 SampleID2 SampleID3 ... SampleID19 SampleID20 +## GENE1 -1.400043517 1.431663588 -1.336606503 . -2.307774531 -2.293199815 +## GENE2 0.255317055 0.171127984 0.089914742 . 0.614199996 -0.335822358 +## GENE3 -2.437263611 2.312015552 0.379995935 . -0.733181166 0.083092829 +## GENE4 -0.005571287 -0.057850207 -0.056034294 . 0.818604632 0.106635015 +## GENE5 0.621552721 -0.975709562 0.700863028 . 0.005259257 1.643080357 +## ... . . . . . . +## GENE49996 0.2027090 0.4424774 0.6336781 . -0.47392601 0.28854415 +## GENE49997 1.2847634 1.2558989 1.2587418 . -2.52268507 -1.77342923 +## GENE49998 0.2648680 1.3883708 -0.3003243 . -1.76756368 0.76883529 +## GENE49999 1.4098422 0.2065422 -0.4955832 . 1.59338432 -0.05131006 +## GENE50000 -0.7546331 0.6750468 0.1188484 . -1.25230132 0.30771323
 MultiAssayExperiment(list(HDF5SE = HDF5SE))
## A MultiAssayExperiment object of 1 listed
@@ -315,9 +278,9 @@ 

Session info
 sessionInfo()

-
## R version 4.3.2 (2023-10-31)
-## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 22.04.3 LTS
+
## R version 4.4.1 (2024-06-14)
+## Platform: x86_64-pc-linux-gnu
+## Running under: Ubuntu 22.04.4 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -339,62 +302,51 @@ 

Session info## [8] base ## ## other attached packages: -## [1] HDF5Array_1.30.0 rhdf5_2.46.1 -## [3] DelayedArray_0.28.0 SparseArray_1.2.3 -## [5] S4Arrays_1.2.0 abind_1.4-5 -## [7] Matrix_1.6-5 MultiAssayExperiment_1.28.0 -## [9] SummarizedExperiment_1.32.0 Biobase_2.62.0 -## [11] GenomicRanges_1.54.1 GenomeInfoDb_1.38.5 -## [13] IRanges_2.36.0 S4Vectors_0.40.2 -## [15] BiocGenerics_0.48.1 MatrixGenerics_1.14.0 -## [17] matrixStats_1.2.0 BiocStyle_2.30.0 +## [1] HDF5Array_1.32.1 rhdf5_2.48.0 +## [3] DelayedArray_0.30.1 SparseArray_1.4.8 +## [5] S4Arrays_1.4.1 abind_1.4-5 +## [7] Matrix_1.7-0 MultiAssayExperiment_1.30.3 +## [9] SummarizedExperiment_1.34.0 Biobase_2.64.0 +## [11] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 +## [13] IRanges_2.38.1 S4Vectors_0.42.1 +## [15] BiocGenerics_0.50.0 MatrixGenerics_1.16.0 +## [17] matrixStats_1.3.0 BiocStyle_2.32.1 ## ## loaded via a namespace (and not attached): -## [1] sass_0.4.8 bitops_1.0-7 stringi_1.8.3 -## [4] lattice_0.22-5 digest_0.6.34 magrittr_2.0.3 -## [7] evaluate_0.23 grid_4.3.2 bookdown_0.37 -## [10] fastmap_1.1.1 jsonlite_1.8.8 BiocManager_1.30.22 -## [13] purrr_1.0.2 textshaping_0.3.7 jquerylib_0.1.4 -## [16] cli_3.6.2 rlang_1.1.3 crayon_1.5.2 -## [19] XVector_0.42.0 cachem_1.0.8 yaml_2.3.8 -## [22] tools_4.3.2 memoise_2.0.1 Rhdf5lib_1.24.1 -## [25] GenomeInfoDbData_1.2.11 vctrs_0.6.5 R6_2.5.1 -## [28] lifecycle_1.0.4 zlibbioc_1.48.0 stringr_1.5.1 -## [31] fs_1.6.3 ragg_1.2.7 desc_1.4.3 -## [34] pkgdown_2.0.7 bslib_0.6.1 glue_1.7.0 -## [37] systemfonts_1.0.5 xfun_0.41 rhdf5filters_1.14.1 -## [40] knitr_1.45 htmltools_0.5.7 rmarkdown_2.25 -## [43] compiler_4.3.2 RCurl_1.98-1.14

+## [1] sass_0.4.9 lattice_0.22-6 digest_0.6.36 +## [4] evaluate_0.24.0 grid_4.4.1 bookdown_0.40 +## [7] fastmap_1.2.0 jsonlite_1.8.8 BiocManager_1.30.23 +## [10] httr_1.4.7 UCSC.utils_1.0.0 textshaping_0.4.0 +## [13] jquerylib_0.1.4 cli_3.6.3 rlang_1.1.4 +## [16] crayon_1.5.3 XVector_0.44.0 cachem_1.1.0 +## [19] yaml_2.3.10 tools_4.4.1 Rhdf5lib_1.26.0 +## [22] GenomeInfoDbData_1.2.12 R6_2.5.1 lifecycle_1.0.4 +## [25] zlibbioc_1.50.0 fs_1.6.4 htmlwidgets_1.6.4 +## [28] ragg_1.3.2 desc_1.4.3 pkgdown_2.1.0 +## [31] bslib_0.8.0 systemfonts_1.1.0 xfun_0.46 +## [34] knitr_1.48 rhdf5filters_1.16.0 htmltools_0.5.8.1 +## [37] rmarkdown_2.27 compiler_4.4.1
-
- - -
- -
- - + diff --git a/articles/extras/MAE-curatedMetagenomicData.html b/articles/extras/MAE-curatedMetagenomicData.html index cd7a2b04..ea097a0e 100644 --- a/articles/extras/MAE-curatedMetagenomicData.html +++ b/articles/extras/MAE-curatedMetagenomicData.html @@ -4,107 +4,71 @@ - + Making use of curatedMetagenomicData • MultiAssayExperiment - - - - - - - - + + + + + - - + + Skip to contents -
-
-
-

Create the MultiAssayExperiment:

 library(MultiAssayExperiment)
 cmd <- MultiAssayExperiment(experiments=esetlist, 
-    colData=colData(as(esetlist[[2]], "SummarizedExperiment")))
+    colData=colData(as(esetlist[[2]], "SummarizedExperiment")))
 cmd
-rownames(cmd)
+rownames(cmd)

CCA with omicade4

 library(omicade4)
-cmdsub <- cmd[, cmd$disease %in% c("adenoma", "CRC", "healthy"), ]
+cmdsub <- cmd[, cmd$disease %in% c("adenoma", "CRC", "healthy"), ]
 ##Get rid of rows that are all zero:
-cmdsub <- cmdsub[lapply(assays(cmdsub), function(exper) rowSums(exper) > 0), ]
+cmdsub <- cmdsub[lapply(assays(cmdsub), function(exper) rowSums(exper) > 0), ]
 
 mcoin <- mcia(assay(cmdsub))
 plot(mcoin, phenovec=cmdsub$disease, sample.lab=FALSE)
@@ -148,7 +112,7 @@

iClusterPlus
 library(iClusterPlus)
 datasets = assay(cmdsub)
-datasets = lapply(datasets, t)
+datasets = lapply(datasets, t)
 iclus = iCluster(datasets=datasets, k=5, lambda=c(0.2, 0.2))
 plotiCluster(fit=iclus, label=cmdsub$disease)

@@ -171,35 +135,26 @@

Others to trylibrary(MCIA) # library(Rtopper) # gene set analysis

- - - - - - - - + diff --git a/articles/index.html b/articles/index.html index b8f9f9cc..c2c8d935 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,108 +1,73 @@ -Articles • MultiAssayExperiment - - -
-
-
- + + +
+
+ -
+
-
+ - - diff --git a/authors.html b/authors.html index 7302d383..ec860cc8 100644 --- a/authors.html +++ b/authors.html @@ -1,129 +1,116 @@ -Authors and Citation • MultiAssayExperiment - - -
-
-
-
- - - +
+ + +
+
+
+
+ +
+

Authors

+
  • Marcel Ramos. Author, maintainer.

  • -

    Levi Waldron. Author. +

    Martin Morgan. Author, contributor. +

    +
  • +
  • +

    Lori Shepherd. Contributor.

  • -

    MultiAssay SIG. Contributor. +

    Hervé Pagès. Contributor. +

    +
  • +
  • +

    Vincent J Carey. Author, contributor. +

    +
  • +
  • +

    Levi Waldron. Author. +

    +
  • +
  • +

    MultiAssay SIG. Contributor.

-
-
-

Citation

- Source: inst/CITATION -
-
+
+

Citation

+

Source: inst/CITATION

-

Marcel Ramos et al. Software For The Integration Of Multiomics Experiments In Bioconductor. Cancer Research, 2017 November 1; 77(21); e39-42. DOI: 10.1158/0008-5472.CAN-17-0344

-
@Article{,
+      

Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez Cabrera C, Chan T, Chapman P, Davis S, Gomez-Cabrero D, Culhane A, Haibe-Kains B, Hansen K, Kodali H, Louis M, Mer A, Reister M, Morgan M, Carey V, Waldron L (2017). +“Software For The Integration Of Multi-Omics Experiments In Bioconductor.” +Cancer Research, 77(21), e39-42. +doi:10.1158/0008-5472.CAN-17-0344, https://cancerres.aacrjournals.org/content/77/21/e39. +

+
@Article{,
   title = {Software For The Integration Of Multi-Omics Experiments In Bioconductor},
-  author = {Marcel Ramos and Lucas Schiffer and Angela Re and Rimsha Azhar and Azfar Basunia and Carmen Rodriguez Cabrera and Tiffany Chan and Philip Chapman and Sean Davis and David Gomez-Cabrero and Aedin C. Culhane and Benjamin Haibe-Kains and Kasper Hansen and Hanish Kodali and Marie Stephie Louis and Arvind Singh Mer and Markus Reister and Martin Morgan and Vincent Carey and Levi Waldron},
+  author = {Marcel Ramos and Lucas Schiffer and Angela Re and Rimsha Azhar and Azfar Basunia and Carmen {Rodriguez Cabrera} and Tiffany Chan and Philip Chapman and Sean Davis and David Gomez-Cabrero and Aedin C. Culhane and Benjamin Haibe-Kains and Kasper Hansen and Hanish Kodali and Marie S Louis and Arvind S Mer and Markus Reister and Martin Morgan and Vincent J Carey and Levi Waldron},
   journal = {Cancer Research},
   year = {2017},
-  volume = {77(21); e39-42},
+  volume = {77},
+  number = {21},
+  pages = {e39-42},
+  doi = {10.1158/0008-5472.CAN-17-0344},
+  url = {https://cancerres.aacrjournals.org/content/77/21/e39},
 }
+
-
- -
- +
-
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H{constructor(t){super(),this._config=this._getConfig(t),this._isAppended=!1,this._element=null}static get Default(){return Xi}static get DefaultType(){return Yi}static get NAME(){return Vi}show(t){if(!this._config.isVisible)return void g(t);this._append();const e=this._getElement();this._config.isAnimated&&d(e),e.classList.add(Ki),this._emulateAnimation((()=>{g(t)}))}hide(t){this._config.isVisible?(this._getElement().classList.remove(Ki),this._emulateAnimation((()=>{this.dispose(),g(t)}))):g(t)}dispose(){this._isAppended&&(N.off(this._element,Qi),this._element.remove(),this._isAppended=!1)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_configAfterMerge(t){return t.rootElement=r(t.rootElement),t}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),N.on(t,Qi,(()=>{g(this._config.clickCallback)})),this._isAppended=!0}_emulateAnimation(t){_(t,this._getElement(),this._config.isAnimated)}}const Gi=".bs.focustrap",Ji=`focusin${Gi}`,Zi=`keydown.tab${Gi}`,tn="backward",en={autofocus:!0,trapElement:null},nn={autofocus:"boolean",trapElement:"element"};class sn extends H{constructor(t){super(),this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return en}static get DefaultType(){return nn}static get NAME(){return"focustrap"}activate(){this._isActive||(this._config.autofocus&&this._config.trapElement.focus(),N.off(document,Gi),N.on(document,Ji,(t=>this._handleFocusin(t))),N.on(document,Zi,(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,N.off(document,Gi))}_handleFocusin(t){const{trapElement:e}=this._config;if(t.target===document||t.target===e||e.contains(t.target))return;const i=z.focusableChildren(e);0===i.length?e.focus():this._lastTabNavDirection===tn?i[i.length-1].focus():i[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?tn:"forward")}}const on=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",rn=".sticky-top",an="padding-right",ln="margin-right";class cn{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,an,(e=>e+t)),this._setElementAttributes(on,an,(e=>e+t)),this._setElementAttributes(rn,ln,(e=>e-t))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,an),this._resetElementAttributes(on,an),this._resetElementAttributes(rn,ln)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t).getPropertyValue(e);t.style.setProperty(e,`${i(Number.parseFloat(s))}px`)}))}_saveInitialAttribute(t,e){const i=t.style.getPropertyValue(e);i&&F.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=F.getDataAttribute(t,e);null!==i?(F.removeDataAttribute(t,e),t.style.setProperty(e,i)):t.style.removeProperty(e)}))}_applyManipulationCallback(t,e){if(o(t))e(t);else for(const i of z.find(t,this._element))e(i)}}const hn=".bs.modal",dn=`hide${hn}`,un=`hidePrevented${hn}`,fn=`hidden${hn}`,pn=`show${hn}`,mn=`shown${hn}`,gn=`resize${hn}`,_n=`click.dismiss${hn}`,bn=`mousedown.dismiss${hn}`,vn=`keydown.dismiss${hn}`,yn=`click${hn}.data-api`,wn="modal-open",An="show",En="modal-static",Tn={backdrop:!0,focus:!0,keyboard:!0},Cn={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class On extends W{constructor(t,e){super(t,e),this._dialog=z.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new cn,this._addEventListeners()}static get Default(){return Tn}static get DefaultType(){return Cn}static get NAME(){return"modal"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||N.trigger(this._element,pn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(wn),this._adjustDialog(),this._backdrop.show((()=>this._showElement(t))))}hide(){this._isShown&&!this._isTransitioning&&(N.trigger(this._element,dn).defaultPrevented||(this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(An),this._queueCallback((()=>this._hideModal()),this._element,this._isAnimated())))}dispose(){N.off(window,hn),N.off(this._dialog,hn),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new Ui({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_showElement(t){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const e=z.findOne(".modal-body",this._dialog);e&&(e.scrollTop=0),d(this._element),this._element.classList.add(An),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,N.trigger(this._element,mn,{relatedTarget:t})}),this._dialog,this._isAnimated())}_addEventListeners(){N.on(this._element,vn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():this._triggerBackdropTransition())})),N.on(window,gn,(()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()})),N.on(this._element,bn,(t=>{N.one(this._element,_n,(e=>{this._element===t.target&&this._element===e.target&&("static"!==this._config.backdrop?this._config.backdrop&&this.hide():this._triggerBackdropTransition())}))}))}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(wn),this._resetAdjustments(),this._scrollBar.reset(),N.trigger(this._element,fn)}))}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(N.trigger(this._element,un).defaultPrevented)return;const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._element.style.overflowY;"hidden"===e||this._element.classList.contains(En)||(t||(this._element.style.overflowY="hidden"),this._element.classList.add(En),this._queueCallback((()=>{this._element.classList.remove(En),this._queueCallback((()=>{this._element.style.overflowY=e}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;if(i&&!t){const t=p()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!i&&t){const t=p()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=On.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}N.on(document,yn,'[data-bs-toggle="modal"]',(function(t){const e=z.getElementFromSelector(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),N.one(e,pn,(t=>{t.defaultPrevented||N.one(e,fn,(()=>{a(this)&&this.focus()}))}));const i=z.findOne(".modal.show");i&&On.getInstance(i).hide(),On.getOrCreateInstance(e).toggle(this)})),R(On),m(On);const xn=".bs.offcanvas",kn=".data-api",Ln=`load${xn}${kn}`,Sn="show",Dn="showing",$n="hiding",In=".offcanvas.show",Nn=`show${xn}`,Pn=`shown${xn}`,Mn=`hide${xn}`,jn=`hidePrevented${xn}`,Fn=`hidden${xn}`,Hn=`resize${xn}`,Wn=`click${xn}${kn}`,Bn=`keydown.dismiss${xn}`,zn={backdrop:!0,keyboard:!0,scroll:!1},Rn={backdrop:"(boolean|string)",keyboard:"boolean",scroll:"boolean"};class qn extends W{constructor(t,e){super(t,e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return zn}static get DefaultType(){return Rn}static get NAME(){return"offcanvas"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||N.trigger(this._element,Nn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._backdrop.show(),this._config.scroll||(new cn).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(Dn),this._queueCallback((()=>{this._config.scroll&&!this._config.backdrop||this._focustrap.activate(),this._element.classList.add(Sn),this._element.classList.remove(Dn),N.trigger(this._element,Pn,{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(N.trigger(this._element,Mn).defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add($n),this._backdrop.hide(),this._queueCallback((()=>{this._element.classList.remove(Sn,$n),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new cn).reset(),N.trigger(this._element,Fn)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const t=Boolean(this._config.backdrop);return new Ui({className:"offcanvas-backdrop",isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?()=>{"static"!==this._config.backdrop?this.hide():N.trigger(this._element,jn)}:null})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_addEventListeners(){N.on(this._element,Bn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():N.trigger(this._element,jn))}))}static jQueryInterface(t){return this.each((function(){const e=qn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}N.on(document,Wn,'[data-bs-toggle="offcanvas"]',(function(t){const e=z.getElementFromSelector(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this))return;N.one(e,Fn,(()=>{a(this)&&this.focus()}));const i=z.findOne(In);i&&i!==e&&qn.getInstance(i).hide(),qn.getOrCreateInstance(e).toggle(this)})),N.on(window,Ln,(()=>{for(const t of z.find(In))qn.getOrCreateInstance(t).show()})),N.on(window,Hn,(()=>{for(const t of z.find("[aria-modal][class*=show][class*=offcanvas-]"))"fixed"!==getComputedStyle(t).position&&qn.getOrCreateInstance(t).hide()})),R(qn),m(qn);const Vn={"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},Kn=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Qn=/^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i,Xn=(t,e)=>{const i=t.nodeName.toLowerCase();return e.includes(i)?!Kn.has(i)||Boolean(Qn.test(t.nodeValue)):e.filter((t=>t instanceof RegExp)).some((t=>t.test(i)))},Yn={allowList:Vn,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"
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")),e}_typeCheckConfig(t){super._typeCheckConfig(t),this._checkContent(t.content)}_checkContent(t){for(const[e,i]of Object.entries(t))super._typeCheckConfig({selector:e,entry:i},Gn)}_setContent(t,e,i){const n=z.findOne(i,t);n&&((e=this._resolvePossibleFunction(e))?o(e)?this._putElementInTemplate(r(e),n):this._config.html?n.innerHTML=this._maybeSanitize(e):n.textContent=e:n.remove())}_maybeSanitize(t){return this._config.sanitize?function(t,e,i){if(!t.length)return t;if(i&&"function"==typeof i)return i(t);const n=(new window.DOMParser).parseFromString(t,"text/html"),s=[].concat(...n.body.querySelectorAll("*"));for(const t of s){const i=t.nodeName.toLowerCase();if(!Object.keys(e).includes(i)){t.remove();continue}const n=[].concat(...t.attributes),s=[].concat(e["*"]||[],e[i]||[]);for(const e of n)Xn(e,s)||t.removeAttribute(e.nodeName)}return n.body.innerHTML}(t,this._config.allowList,this._config.sanitizeFn):t}_resolvePossibleFunction(t){return g(t,[this])}_putElementInTemplate(t,e){if(this._config.html)return e.innerHTML="",void e.append(t);e.textContent=t.textContent}}const Zn=new Set(["sanitize","allowList","sanitizeFn"]),ts="fade",es="show",is=".modal",ns="hide.bs.modal",ss="hover",os="focus",rs={AUTO:"auto",TOP:"top",RIGHT:p()?"left":"right",BOTTOM:"bottom",LEFT:p()?"right":"left"},as={allowList:Vn,animation:!0,boundary:"clippingParents",container:!1,customClass:"",delay:0,fallbackPlacements:["top","right","bottom","left"],html:!1,offset:[0,6],placement:"top",popperConfig:null,sanitize:!0,sanitizeFn:null,selector:!1,template:'',title:"",trigger:"hover focus"},ls={allowList:"object",animation:"boolean",boundary:"(string|element)",container:"(string|element|boolean)",customClass:"(string|function)",delay:"(number|object)",fallbackPlacements:"array",html:"boolean",offset:"(array|string|function)",placement:"(string|function)",popperConfig:"(null|object|function)",sanitize:"boolean",sanitizeFn:"(null|function)",selector:"(string|boolean)",template:"string",title:"(string|element|function)",trigger:"string"};class cs extends W{constructor(t,e){if(void 0===vi)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t,e),this._isEnabled=!0,this._timeout=0,this._isHovered=null,this._activeTrigger={},this._popper=null,this._templateFactory=null,this._newContent=null,this.tip=null,this._setListeners(),this._config.selector||this._fixTitle()}static get Default(){return as}static get DefaultType(){return ls}static get NAME(){return"tooltip"}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(){this._isEnabled&&(this._activeTrigger.click=!this._activeTrigger.click,this._isShown()?this._leave():this._enter())}dispose(){clearTimeout(this._timeout),N.off(this._element.closest(is),ns,this._hideModalHandler),this._element.getAttribute("data-bs-original-title")&&this._element.setAttribute("title",this._element.getAttribute("data-bs-original-title")),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this._isWithContent()||!this._isEnabled)return;const t=N.trigger(this._element,this.constructor.eventName("show")),e=(c(this._element)||this._element.ownerDocument.documentElement).contains(this._element);if(t.defaultPrevented||!e)return;this._disposePopper();const i=this._getTipElement();this._element.setAttribute("aria-describedby",i.getAttribute("id"));const{container:n}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(n.append(i),N.trigger(this._element,this.constructor.eventName("inserted"))),this._popper=this._createPopper(i),i.classList.add(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._queueCallback((()=>{N.trigger(this._element,this.constructor.eventName("shown")),!1===this._isHovered&&this._leave(),this._isHovered=!1}),this.tip,this._isAnimated())}hide(){if(this._isShown()&&!N.trigger(this._element,this.constructor.eventName("hide")).defaultPrevented){if(this._getTipElement().classList.remove(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.off(t,"mouseover",h);this._activeTrigger.click=!1,this._activeTrigger[os]=!1,this._activeTrigger[ss]=!1,this._isHovered=null,this._queueCallback((()=>{this._isWithActiveTrigger()||(this._isHovered||this._disposePopper(),this._element.removeAttribute("aria-describedby"),N.trigger(this._element,this.constructor.eventName("hidden")))}),this.tip,this._isAnimated())}}update(){this._popper&&this._popper.update()}_isWithContent(){return Boolean(this._getTitle())}_getTipElement(){return this.tip||(this.tip=this._createTipElement(this._newContent||this._getContentForTemplate())),this.tip}_createTipElement(t){const e=this._getTemplateFactory(t).toHtml();if(!e)return null;e.classList.remove(ts,es),e.classList.add(`bs-${this.constructor.NAME}-auto`);const i=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME).toString();return e.setAttribute("id",i),this._isAnimated()&&e.classList.add(ts),e}setContent(t){this._newContent=t,this._isShown()&&(this._disposePopper(),this.show())}_getTemplateFactory(t){return this._templateFactory?this._templateFactory.changeContent(t):this._templateFactory=new Jn({...this._config,content:t,extraClass:this._resolvePossibleFunction(this._config.customClass)}),this._templateFactory}_getContentForTemplate(){return{".tooltip-inner":this._getTitle()}}_getTitle(){return this._resolvePossibleFunction(this._config.title)||this._element.getAttribute("data-bs-original-title")}_initializeOnDelegatedTarget(t){return this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_isAnimated(){return this._config.animation||this.tip&&this.tip.classList.contains(ts)}_isShown(){return this.tip&&this.tip.classList.contains(es)}_createPopper(t){const e=g(this._config.placement,[this,t,this._element]),i=rs[e.toUpperCase()];return bi(this._element,t,this._getPopperConfig(i))}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return g(t,[this._element])}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"preSetPlacement",enabled:!0,phase:"beforeMain",fn:t=>{this._getTipElement().setAttribute("data-popper-placement",t.state.placement)}}]};return{...e,...g(this._config.popperConfig,[e])}}_setListeners(){const t=this._config.trigger.split(" ");for(const e of t)if("click"===e)N.on(this._element,this.constructor.eventName("click"),this._config.selector,(t=>{this._initializeOnDelegatedTarget(t).toggle()}));else 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object[0] : object\n }\n\n if (typeof object === 'string' && object.length > 0) {\n return document.querySelector(parseSelector(object))\n }\n\n return null\n}\n\nconst isVisible = element => {\n if (!isElement(element) || element.getClientRects().length === 0) {\n return false\n }\n\n const elementIsVisible = getComputedStyle(element).getPropertyValue('visibility') === 'visible'\n // Handle `details` element as its content may falsie appear visible when it is closed\n const closedDetails = element.closest('details:not([open])')\n\n if (!closedDetails) {\n return elementIsVisible\n }\n\n if (closedDetails !== element) {\n const summary = element.closest('summary')\n if (summary && summary.parentNode !== closedDetails) {\n return false\n }\n\n if (summary === null) {\n return false\n }\n }\n\n return elementIsVisible\n}\n\nconst isDisabled = element => {\n if (!element || element.nodeType !== Node.ELEMENT_NODE) {\n return true\n }\n\n if (element.classList.contains('disabled')) {\n return true\n }\n\n if (typeof element.disabled !== 'undefined') {\n return element.disabled\n }\n\n return element.hasAttribute('disabled') && element.getAttribute('disabled') !== 'false'\n}\n\nconst findShadowRoot = element => {\n if (!document.documentElement.attachShadow) {\n return null\n }\n\n // Can find the shadow root otherwise it'll return the document\n if (typeof element.getRootNode === 'function') {\n const root = element.getRootNode()\n return root instanceof ShadowRoot ? root : null\n }\n\n if (element instanceof ShadowRoot) {\n return element\n }\n\n // when we don't find a shadow root\n if (!element.parentNode) {\n return null\n }\n\n return findShadowRoot(element.parentNode)\n}\n\nconst noop = () => {}\n\n/**\n * Trick to restart an element's animation\n *\n * @param {HTMLElement} element\n * @return void\n *\n * @see https://www.charistheo.io/blog/2021/02/restart-a-css-animation-with-javascript/#restarting-a-css-animation\n */\nconst reflow = element => {\n element.offsetHeight // eslint-disable-line no-unused-expressions\n}\n\nconst getjQuery = () => {\n if (window.jQuery && !document.body.hasAttribute('data-bs-no-jquery')) {\n return window.jQuery\n }\n\n return null\n}\n\nconst DOMContentLoadedCallbacks = []\n\nconst onDOMContentLoaded = callback => {\n if (document.readyState === 'loading') {\n // add listener on the first call when the document is in loading state\n if (!DOMContentLoadedCallbacks.length) {\n document.addEventListener('DOMContentLoaded', () => {\n for (const callback of DOMContentLoadedCallbacks) {\n callback()\n }\n })\n }\n\n DOMContentLoadedCallbacks.push(callback)\n } else {\n callback()\n }\n}\n\nconst isRTL = () => document.documentElement.dir === 'rtl'\n\nconst defineJQueryPlugin = plugin => {\n onDOMContentLoaded(() => {\n const $ = getjQuery()\n /* istanbul ignore if */\n if ($) {\n const name = plugin.NAME\n const JQUERY_NO_CONFLICT = $.fn[name]\n $.fn[name] = plugin.jQueryInterface\n $.fn[name].Constructor = plugin\n $.fn[name].noConflict = () => {\n $.fn[name] = JQUERY_NO_CONFLICT\n return plugin.jQueryInterface\n }\n }\n })\n}\n\nconst execute = (possibleCallback, args = [], defaultValue = possibleCallback) => {\n return typeof possibleCallback === 'function' ? possibleCallback(...args) : defaultValue\n}\n\nconst executeAfterTransition = (callback, transitionElement, waitForTransition = true) => {\n if (!waitForTransition) {\n execute(callback)\n return\n }\n\n const durationPadding = 5\n const emulatedDuration = getTransitionDurationFromElement(transitionElement) + durationPadding\n\n let called = false\n\n const handler = ({ target }) => {\n if (target !== transitionElement) {\n return\n }\n\n called = true\n transitionElement.removeEventListener(TRANSITION_END, handler)\n execute(callback)\n }\n\n transitionElement.addEventListener(TRANSITION_END, handler)\n setTimeout(() => {\n if (!called) {\n triggerTransitionEnd(transitionElement)\n }\n }, emulatedDuration)\n}\n\n/**\n * Return the previous/next element of a list.\n *\n * @param {array} list The list of elements\n * @param activeElement The active element\n * @param shouldGetNext Choose to get next or previous element\n * @param isCycleAllowed\n * @return {Element|elem} The proper element\n */\nconst getNextActiveElement = (list, activeElement, shouldGetNext, isCycleAllowed) => {\n const listLength = list.length\n let index = list.indexOf(activeElement)\n\n // if the element does not exist in the list return an element\n // depending on the direction and if cycle is allowed\n if (index === -1) {\n return !shouldGetNext && isCycleAllowed ? list[listLength - 1] : list[0]\n }\n\n index += shouldGetNext ? 1 : -1\n\n if (isCycleAllowed) {\n index = (index + listLength) % listLength\n }\n\n return list[Math.max(0, Math.min(index, listLength - 1))]\n}\n\nexport {\n defineJQueryPlugin,\n execute,\n executeAfterTransition,\n findShadowRoot,\n getElement,\n getjQuery,\n getNextActiveElement,\n getTransitionDurationFromElement,\n getUID,\n isDisabled,\n isElement,\n isRTL,\n isVisible,\n noop,\n onDOMContentLoaded,\n parseSelector,\n reflow,\n triggerTransitionEnd,\n toType\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap dom/event-handler.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { getjQuery } from '../util/index.js'\n\n/**\n * Constants\n */\n\nconst namespaceRegex = /[^.]*(?=\\..*)\\.|.*/\nconst stripNameRegex = /\\..*/\nconst stripUidRegex = /::\\d+$/\nconst eventRegistry = {} // Events storage\nlet uidEvent = 1\nconst customEvents = {\n mouseenter: 'mouseover',\n mouseleave: 'mouseout'\n}\n\nconst nativeEvents = new Set([\n 'click',\n 'dblclick',\n 'mouseup',\n 'mousedown',\n 'contextmenu',\n 'mousewheel',\n 'DOMMouseScroll',\n 'mouseover',\n 'mouseout',\n 'mousemove',\n 'selectstart',\n 'selectend',\n 'keydown',\n 'keypress',\n 'keyup',\n 'orientationchange',\n 'touchstart',\n 'touchmove',\n 'touchend',\n 'touchcancel',\n 'pointerdown',\n 'pointermove',\n 'pointerup',\n 'pointerleave',\n 'pointercancel',\n 'gesturestart',\n 'gesturechange',\n 'gestureend',\n 'focus',\n 'blur',\n 'change',\n 'reset',\n 'select',\n 'submit',\n 'focusin',\n 'focusout',\n 'load',\n 'unload',\n 'beforeunload',\n 'resize',\n 'move',\n 'DOMContentLoaded',\n 'readystatechange',\n 'error',\n 'abort',\n 'scroll'\n])\n\n/**\n * Private methods\n */\n\nfunction makeEventUid(element, uid) {\n return (uid && `${uid}::${uidEvent++}`) || element.uidEvent || uidEvent++\n}\n\nfunction getElementEvents(element) {\n const uid = makeEventUid(element)\n\n element.uidEvent = uid\n eventRegistry[uid] = eventRegistry[uid] || {}\n\n return eventRegistry[uid]\n}\n\nfunction bootstrapHandler(element, fn) {\n return function handler(event) {\n hydrateObj(event, { delegateTarget: element })\n\n if (handler.oneOff) {\n EventHandler.off(element, event.type, fn)\n }\n\n return fn.apply(element, [event])\n }\n}\n\nfunction bootstrapDelegationHandler(element, selector, fn) {\n return function handler(event) {\n const domElements = element.querySelectorAll(selector)\n\n for (let { target } = event; target && target !== this; target = target.parentNode) {\n for (const domElement of domElements) {\n if (domElement !== target) {\n continue\n }\n\n hydrateObj(event, { delegateTarget: target })\n\n if (handler.oneOff) {\n EventHandler.off(element, event.type, selector, fn)\n }\n\n return fn.apply(target, [event])\n }\n }\n }\n}\n\nfunction findHandler(events, callable, delegationSelector = null) {\n return Object.values(events)\n .find(event => event.callable === callable && event.delegationSelector === delegationSelector)\n}\n\nfunction normalizeParameters(originalTypeEvent, handler, delegationFunction) {\n const isDelegated = typeof handler === 'string'\n // TODO: tooltip passes `false` instead of selector, so we need to check\n const callable = isDelegated ? delegationFunction : (handler || delegationFunction)\n let typeEvent = getTypeEvent(originalTypeEvent)\n\n if (!nativeEvents.has(typeEvent)) {\n typeEvent = originalTypeEvent\n }\n\n return [isDelegated, callable, typeEvent]\n}\n\nfunction addHandler(element, originalTypeEvent, handler, delegationFunction, oneOff) {\n if (typeof originalTypeEvent !== 'string' || !element) {\n return\n }\n\n let [isDelegated, callable, typeEvent] = normalizeParameters(originalTypeEvent, handler, delegationFunction)\n\n // in case of mouseenter or mouseleave wrap the handler within a function that checks for its DOM position\n // this prevents the handler from being dispatched the same way as mouseover or mouseout does\n if (originalTypeEvent in customEvents) {\n const wrapFunction = fn => {\n return function (event) {\n if (!event.relatedTarget || (event.relatedTarget !== event.delegateTarget && !event.delegateTarget.contains(event.relatedTarget))) {\n return fn.call(this, event)\n }\n }\n }\n\n callable = wrapFunction(callable)\n }\n\n const events = getElementEvents(element)\n const handlers = events[typeEvent] || (events[typeEvent] = {})\n const previousFunction = findHandler(handlers, callable, isDelegated ? handler : null)\n\n if (previousFunction) {\n previousFunction.oneOff = previousFunction.oneOff && oneOff\n\n return\n }\n\n const uid = makeEventUid(callable, originalTypeEvent.replace(namespaceRegex, ''))\n const fn = isDelegated ?\n bootstrapDelegationHandler(element, handler, callable) :\n bootstrapHandler(element, callable)\n\n fn.delegationSelector = isDelegated ? handler : null\n fn.callable = callable\n fn.oneOff = oneOff\n fn.uidEvent = uid\n handlers[uid] = fn\n\n element.addEventListener(typeEvent, fn, isDelegated)\n}\n\nfunction removeHandler(element, events, typeEvent, handler, delegationSelector) {\n const fn = findHandler(events[typeEvent], handler, delegationSelector)\n\n if (!fn) {\n return\n }\n\n element.removeEventListener(typeEvent, fn, Boolean(delegationSelector))\n delete events[typeEvent][fn.uidEvent]\n}\n\nfunction removeNamespacedHandlers(element, events, typeEvent, namespace) {\n const storeElementEvent = events[typeEvent] || {}\n\n for (const [handlerKey, event] of Object.entries(storeElementEvent)) {\n if (handlerKey.includes(namespace)) {\n removeHandler(element, events, typeEvent, event.callable, event.delegationSelector)\n }\n }\n}\n\nfunction getTypeEvent(event) {\n // allow to get the native events from namespaced events ('click.bs.button' --> 'click')\n event = event.replace(stripNameRegex, '')\n return customEvents[event] || event\n}\n\nconst EventHandler = {\n on(element, event, handler, delegationFunction) {\n addHandler(element, event, handler, delegationFunction, false)\n },\n\n one(element, event, handler, delegationFunction) {\n addHandler(element, event, handler, delegationFunction, true)\n },\n\n off(element, originalTypeEvent, handler, delegationFunction) {\n if (typeof originalTypeEvent !== 'string' || !element) {\n return\n }\n\n const [isDelegated, callable, typeEvent] = normalizeParameters(originalTypeEvent, handler, delegationFunction)\n const inNamespace = typeEvent !== originalTypeEvent\n const events = getElementEvents(element)\n const storeElementEvent = events[typeEvent] || {}\n const isNamespace = originalTypeEvent.startsWith('.')\n\n if (typeof callable !== 'undefined') {\n // Simplest case: handler is passed, remove that listener ONLY.\n if (!Object.keys(storeElementEvent).length) {\n return\n }\n\n removeHandler(element, events, typeEvent, callable, isDelegated ? handler : null)\n return\n }\n\n if (isNamespace) {\n for (const elementEvent of Object.keys(events)) {\n removeNamespacedHandlers(element, events, elementEvent, originalTypeEvent.slice(1))\n }\n }\n\n for (const [keyHandlers, event] of Object.entries(storeElementEvent)) {\n const handlerKey = keyHandlers.replace(stripUidRegex, '')\n\n if (!inNamespace || originalTypeEvent.includes(handlerKey)) {\n removeHandler(element, events, typeEvent, event.callable, event.delegationSelector)\n }\n }\n },\n\n trigger(element, event, args) {\n if (typeof event !== 'string' || !element) {\n return null\n }\n\n const $ = getjQuery()\n const typeEvent = getTypeEvent(event)\n const inNamespace = event !== typeEvent\n\n let jQueryEvent = null\n let bubbles = true\n let nativeDispatch = true\n let defaultPrevented = false\n\n if (inNamespace && $) {\n jQueryEvent = $.Event(event, args)\n\n $(element).trigger(jQueryEvent)\n bubbles = !jQueryEvent.isPropagationStopped()\n nativeDispatch = !jQueryEvent.isImmediatePropagationStopped()\n defaultPrevented = jQueryEvent.isDefaultPrevented()\n }\n\n const evt = hydrateObj(new Event(event, { bubbles, cancelable: true }), args)\n\n if (defaultPrevented) {\n evt.preventDefault()\n }\n\n if (nativeDispatch) {\n element.dispatchEvent(evt)\n }\n\n if (evt.defaultPrevented && jQueryEvent) {\n jQueryEvent.preventDefault()\n }\n\n return evt\n }\n}\n\nfunction hydrateObj(obj, meta = {}) {\n for (const [key, value] of Object.entries(meta)) {\n try {\n obj[key] = value\n } catch {\n Object.defineProperty(obj, key, {\n configurable: true,\n get() {\n return value\n }\n })\n }\n }\n\n return obj\n}\n\nexport default EventHandler\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap dom/manipulator.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nfunction normalizeData(value) {\n if (value === 'true') {\n return true\n }\n\n if (value === 'false') {\n return false\n }\n\n if (value === Number(value).toString()) {\n return Number(value)\n }\n\n if (value === '' || value === 'null') {\n return null\n }\n\n if (typeof value !== 'string') {\n return value\n }\n\n try {\n return JSON.parse(decodeURIComponent(value))\n } catch {\n return value\n }\n}\n\nfunction normalizeDataKey(key) {\n return key.replace(/[A-Z]/g, chr => `-${chr.toLowerCase()}`)\n}\n\nconst Manipulator = {\n setDataAttribute(element, key, value) {\n element.setAttribute(`data-bs-${normalizeDataKey(key)}`, value)\n },\n\n removeDataAttribute(element, key) {\n element.removeAttribute(`data-bs-${normalizeDataKey(key)}`)\n },\n\n getDataAttributes(element) {\n if (!element) {\n return {}\n }\n\n const attributes = {}\n const bsKeys = Object.keys(element.dataset).filter(key => key.startsWith('bs') && !key.startsWith('bsConfig'))\n\n for (const key of bsKeys) {\n let pureKey = key.replace(/^bs/, '')\n pureKey = pureKey.charAt(0).toLowerCase() + pureKey.slice(1, pureKey.length)\n attributes[pureKey] = normalizeData(element.dataset[key])\n }\n\n return attributes\n },\n\n getDataAttribute(element, key) {\n return normalizeData(element.getAttribute(`data-bs-${normalizeDataKey(key)}`))\n }\n}\n\nexport default Manipulator\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/config.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Manipulator from '../dom/manipulator.js'\nimport { isElement, toType } from './index.js'\n\n/**\n * Class definition\n */\n\nclass Config {\n // Getters\n static get Default() {\n return {}\n }\n\n static get DefaultType() {\n return {}\n }\n\n static get NAME() {\n throw new Error('You have to implement the static method \"NAME\", for each component!')\n }\n\n _getConfig(config) {\n config = this._mergeConfigObj(config)\n config = this._configAfterMerge(config)\n this._typeCheckConfig(config)\n return config\n }\n\n _configAfterMerge(config) {\n return config\n }\n\n _mergeConfigObj(config, element) {\n const jsonConfig = isElement(element) ? Manipulator.getDataAttribute(element, 'config') : {} // try to parse\n\n return {\n ...this.constructor.Default,\n ...(typeof jsonConfig === 'object' ? jsonConfig : {}),\n ...(isElement(element) ? Manipulator.getDataAttributes(element) : {}),\n ...(typeof config === 'object' ? config : {})\n }\n }\n\n _typeCheckConfig(config, configTypes = this.constructor.DefaultType) {\n for (const [property, expectedTypes] of Object.entries(configTypes)) {\n const value = config[property]\n const valueType = isElement(value) ? 'element' : toType(value)\n\n if (!new RegExp(expectedTypes).test(valueType)) {\n throw new TypeError(\n `${this.constructor.NAME.toUpperCase()}: Option \"${property}\" provided type \"${valueType}\" but expected type \"${expectedTypes}\".`\n )\n }\n }\n }\n}\n\nexport default Config\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap base-component.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Data from './dom/data.js'\nimport EventHandler from './dom/event-handler.js'\nimport Config from './util/config.js'\nimport { executeAfterTransition, getElement } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst VERSION = '5.3.1'\n\n/**\n * Class definition\n */\n\nclass BaseComponent extends Config {\n constructor(element, config) {\n super()\n\n element = getElement(element)\n if (!element) {\n return\n }\n\n this._element = element\n this._config = this._getConfig(config)\n\n Data.set(this._element, this.constructor.DATA_KEY, this)\n }\n\n // Public\n dispose() {\n Data.remove(this._element, this.constructor.DATA_KEY)\n EventHandler.off(this._element, this.constructor.EVENT_KEY)\n\n for (const propertyName of Object.getOwnPropertyNames(this)) {\n this[propertyName] = null\n }\n }\n\n _queueCallback(callback, element, isAnimated = true) {\n executeAfterTransition(callback, element, isAnimated)\n }\n\n _getConfig(config) {\n config = this._mergeConfigObj(config, this._element)\n config = this._configAfterMerge(config)\n this._typeCheckConfig(config)\n return config\n }\n\n // Static\n static getInstance(element) {\n return Data.get(getElement(element), this.DATA_KEY)\n }\n\n static getOrCreateInstance(element, config = {}) {\n return this.getInstance(element) || new this(element, typeof config === 'object' ? config : null)\n }\n\n static get VERSION() {\n return VERSION\n }\n\n static get DATA_KEY() {\n return `bs.${this.NAME}`\n }\n\n static get EVENT_KEY() {\n return `.${this.DATA_KEY}`\n }\n\n static eventName(name) {\n return `${name}${this.EVENT_KEY}`\n }\n}\n\nexport default BaseComponent\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap dom/selector-engine.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { isDisabled, isVisible, parseSelector } from '../util/index.js'\n\nconst getSelector = element => {\n let selector = element.getAttribute('data-bs-target')\n\n if (!selector || selector === '#') {\n let hrefAttribute = element.getAttribute('href')\n\n // The only valid content that could double as a selector are IDs or classes,\n // so everything starting with `#` or `.`. If a \"real\" URL is used as the selector,\n // `document.querySelector` will rightfully complain it is invalid.\n // See https://github.com/twbs/bootstrap/issues/32273\n if (!hrefAttribute || (!hrefAttribute.includes('#') && !hrefAttribute.startsWith('.'))) {\n return null\n }\n\n // Just in case some CMS puts out a full URL with the anchor appended\n if (hrefAttribute.includes('#') && !hrefAttribute.startsWith('#')) {\n hrefAttribute = `#${hrefAttribute.split('#')[1]}`\n }\n\n selector = hrefAttribute && hrefAttribute !== '#' ? hrefAttribute.trim() : null\n }\n\n return parseSelector(selector)\n}\n\nconst SelectorEngine = {\n find(selector, element = document.documentElement) {\n return [].concat(...Element.prototype.querySelectorAll.call(element, selector))\n },\n\n findOne(selector, element = document.documentElement) {\n return Element.prototype.querySelector.call(element, selector)\n },\n\n children(element, selector) {\n return [].concat(...element.children).filter(child => child.matches(selector))\n },\n\n parents(element, selector) {\n const parents = []\n let ancestor = element.parentNode.closest(selector)\n\n while (ancestor) {\n parents.push(ancestor)\n ancestor = ancestor.parentNode.closest(selector)\n }\n\n return parents\n },\n\n prev(element, selector) {\n let previous = element.previousElementSibling\n\n while (previous) {\n if (previous.matches(selector)) {\n return [previous]\n }\n\n previous = previous.previousElementSibling\n }\n\n return []\n },\n // TODO: this is now unused; remove later along with prev()\n next(element, selector) {\n let next = element.nextElementSibling\n\n while (next) {\n if (next.matches(selector)) {\n return [next]\n }\n\n next = next.nextElementSibling\n }\n\n return []\n },\n\n focusableChildren(element) {\n const focusables = [\n 'a',\n 'button',\n 'input',\n 'textarea',\n 'select',\n 'details',\n '[tabindex]',\n '[contenteditable=\"true\"]'\n ].map(selector => `${selector}:not([tabindex^=\"-\"])`).join(',')\n\n return this.find(focusables, element).filter(el => !isDisabled(el) && isVisible(el))\n },\n\n getSelectorFromElement(element) {\n const selector = getSelector(element)\n\n if (selector) {\n return SelectorEngine.findOne(selector) ? selector : null\n }\n\n return null\n },\n\n getElementFromSelector(element) {\n const selector = getSelector(element)\n\n return selector ? SelectorEngine.findOne(selector) : null\n },\n\n getMultipleElementsFromSelector(element) {\n const selector = getSelector(element)\n\n return selector ? SelectorEngine.find(selector) : []\n }\n}\n\nexport default SelectorEngine\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/component-functions.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport SelectorEngine from '../dom/selector-engine.js'\nimport { isDisabled } from './index.js'\n\nconst enableDismissTrigger = (component, method = 'hide') => {\n const clickEvent = `click.dismiss${component.EVENT_KEY}`\n const name = component.NAME\n\n EventHandler.on(document, clickEvent, `[data-bs-dismiss=\"${name}\"]`, function (event) {\n if (['A', 'AREA'].includes(this.tagName)) {\n event.preventDefault()\n }\n\n if (isDisabled(this)) {\n return\n }\n\n const target = SelectorEngine.getElementFromSelector(this) || this.closest(`.${name}`)\n const instance = component.getOrCreateInstance(target)\n\n // Method argument is left, for Alert and only, as it doesn't implement the 'hide' method\n instance[method]()\n })\n}\n\nexport {\n enableDismissTrigger\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap alert.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport { defineJQueryPlugin } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'alert'\nconst DATA_KEY = 'bs.alert'\nconst EVENT_KEY = `.${DATA_KEY}`\n\nconst EVENT_CLOSE = `close${EVENT_KEY}`\nconst EVENT_CLOSED = `closed${EVENT_KEY}`\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\n\n/**\n * Class definition\n */\n\nclass Alert extends BaseComponent {\n // Getters\n static get NAME() {\n return NAME\n }\n\n // Public\n close() {\n const closeEvent = EventHandler.trigger(this._element, EVENT_CLOSE)\n\n if (closeEvent.defaultPrevented) {\n return\n }\n\n this._element.classList.remove(CLASS_NAME_SHOW)\n\n const isAnimated = this._element.classList.contains(CLASS_NAME_FADE)\n this._queueCallback(() => this._destroyElement(), this._element, isAnimated)\n }\n\n // Private\n _destroyElement() {\n this._element.remove()\n EventHandler.trigger(this._element, EVENT_CLOSED)\n this.dispose()\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Alert.getOrCreateInstance(this)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config](this)\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nenableDismissTrigger(Alert, 'close')\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Alert)\n\nexport default Alert\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap button.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport { defineJQueryPlugin } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'button'\nconst DATA_KEY = 'bs.button'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst CLASS_NAME_ACTIVE = 'active'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"button\"]'\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\n/**\n * Class definition\n */\n\nclass Button extends BaseComponent {\n // Getters\n static get NAME() {\n return NAME\n }\n\n // Public\n toggle() {\n // Toggle class and sync the `aria-pressed` attribute with the return value of the `.toggle()` method\n this._element.setAttribute('aria-pressed', this._element.classList.toggle(CLASS_NAME_ACTIVE))\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Button.getOrCreateInstance(this)\n\n if (config === 'toggle') {\n data[config]()\n }\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, event => {\n event.preventDefault()\n\n const button = event.target.closest(SELECTOR_DATA_TOGGLE)\n const data = Button.getOrCreateInstance(button)\n\n data.toggle()\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Button)\n\nexport default Button\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/swipe.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport Config from './config.js'\nimport { execute } from './index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'swipe'\nconst EVENT_KEY = '.bs.swipe'\nconst EVENT_TOUCHSTART = `touchstart${EVENT_KEY}`\nconst EVENT_TOUCHMOVE = `touchmove${EVENT_KEY}`\nconst EVENT_TOUCHEND = `touchend${EVENT_KEY}`\nconst EVENT_POINTERDOWN = `pointerdown${EVENT_KEY}`\nconst EVENT_POINTERUP = `pointerup${EVENT_KEY}`\nconst POINTER_TYPE_TOUCH = 'touch'\nconst POINTER_TYPE_PEN = 'pen'\nconst CLASS_NAME_POINTER_EVENT = 'pointer-event'\nconst SWIPE_THRESHOLD = 40\n\nconst Default = {\n endCallback: null,\n leftCallback: null,\n rightCallback: null\n}\n\nconst DefaultType = {\n endCallback: '(function|null)',\n leftCallback: '(function|null)',\n rightCallback: '(function|null)'\n}\n\n/**\n * Class definition\n */\n\nclass Swipe extends Config {\n constructor(element, config) {\n super()\n this._element = element\n\n if (!element || !Swipe.isSupported()) {\n return\n }\n\n this._config = this._getConfig(config)\n this._deltaX = 0\n this._supportPointerEvents = Boolean(window.PointerEvent)\n this._initEvents()\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n dispose() {\n EventHandler.off(this._element, EVENT_KEY)\n }\n\n // Private\n _start(event) {\n if (!this._supportPointerEvents) {\n this._deltaX = event.touches[0].clientX\n\n return\n }\n\n if (this._eventIsPointerPenTouch(event)) {\n this._deltaX = event.clientX\n }\n }\n\n _end(event) {\n if (this._eventIsPointerPenTouch(event)) {\n this._deltaX = event.clientX - this._deltaX\n }\n\n this._handleSwipe()\n execute(this._config.endCallback)\n }\n\n _move(event) {\n this._deltaX = event.touches && event.touches.length > 1 ?\n 0 :\n event.touches[0].clientX - this._deltaX\n }\n\n _handleSwipe() {\n const absDeltaX = Math.abs(this._deltaX)\n\n if (absDeltaX <= SWIPE_THRESHOLD) {\n return\n }\n\n const direction = absDeltaX / this._deltaX\n\n this._deltaX = 0\n\n if (!direction) {\n return\n }\n\n execute(direction > 0 ? this._config.rightCallback : this._config.leftCallback)\n }\n\n _initEvents() {\n if (this._supportPointerEvents) {\n EventHandler.on(this._element, EVENT_POINTERDOWN, event => this._start(event))\n EventHandler.on(this._element, EVENT_POINTERUP, event => this._end(event))\n\n this._element.classList.add(CLASS_NAME_POINTER_EVENT)\n } else {\n EventHandler.on(this._element, EVENT_TOUCHSTART, event => this._start(event))\n EventHandler.on(this._element, EVENT_TOUCHMOVE, event => this._move(event))\n EventHandler.on(this._element, EVENT_TOUCHEND, event => this._end(event))\n }\n }\n\n _eventIsPointerPenTouch(event) {\n return this._supportPointerEvents && (event.pointerType === POINTER_TYPE_PEN || event.pointerType === POINTER_TYPE_TOUCH)\n }\n\n // Static\n static isSupported() {\n return 'ontouchstart' in document.documentElement || navigator.maxTouchPoints > 0\n }\n}\n\nexport default Swipe\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap carousel.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport Manipulator from './dom/manipulator.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport {\n defineJQueryPlugin,\n getNextActiveElement,\n isRTL,\n isVisible,\n reflow,\n triggerTransitionEnd\n} from './util/index.js'\nimport Swipe from './util/swipe.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'carousel'\nconst DATA_KEY = 'bs.carousel'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst ARROW_LEFT_KEY = 'ArrowLeft'\nconst ARROW_RIGHT_KEY = 'ArrowRight'\nconst TOUCHEVENT_COMPAT_WAIT = 500 // Time for mouse compat events to fire after touch\n\nconst ORDER_NEXT = 'next'\nconst ORDER_PREV = 'prev'\nconst DIRECTION_LEFT = 'left'\nconst DIRECTION_RIGHT = 'right'\n\nconst EVENT_SLIDE = `slide${EVENT_KEY}`\nconst EVENT_SLID = `slid${EVENT_KEY}`\nconst EVENT_KEYDOWN = `keydown${EVENT_KEY}`\nconst EVENT_MOUSEENTER = `mouseenter${EVENT_KEY}`\nconst EVENT_MOUSELEAVE = `mouseleave${EVENT_KEY}`\nconst EVENT_DRAG_START = `dragstart${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_CAROUSEL = 'carousel'\nconst CLASS_NAME_ACTIVE = 'active'\nconst CLASS_NAME_SLIDE = 'slide'\nconst CLASS_NAME_END = 'carousel-item-end'\nconst CLASS_NAME_START = 'carousel-item-start'\nconst CLASS_NAME_NEXT = 'carousel-item-next'\nconst CLASS_NAME_PREV = 'carousel-item-prev'\n\nconst SELECTOR_ACTIVE = '.active'\nconst SELECTOR_ITEM = '.carousel-item'\nconst SELECTOR_ACTIVE_ITEM = SELECTOR_ACTIVE + SELECTOR_ITEM\nconst SELECTOR_ITEM_IMG = '.carousel-item img'\nconst SELECTOR_INDICATORS = '.carousel-indicators'\nconst SELECTOR_DATA_SLIDE = '[data-bs-slide], [data-bs-slide-to]'\nconst SELECTOR_DATA_RIDE = '[data-bs-ride=\"carousel\"]'\n\nconst KEY_TO_DIRECTION = {\n [ARROW_LEFT_KEY]: DIRECTION_RIGHT,\n [ARROW_RIGHT_KEY]: DIRECTION_LEFT\n}\n\nconst Default = {\n interval: 5000,\n keyboard: true,\n pause: 'hover',\n ride: false,\n touch: true,\n wrap: true\n}\n\nconst DefaultType = {\n interval: '(number|boolean)', // TODO:v6 remove boolean support\n keyboard: 'boolean',\n pause: '(string|boolean)',\n ride: '(boolean|string)',\n touch: 'boolean',\n wrap: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Carousel extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._interval = null\n this._activeElement = null\n this._isSliding = false\n this.touchTimeout = null\n this._swipeHelper = null\n\n this._indicatorsElement = SelectorEngine.findOne(SELECTOR_INDICATORS, this._element)\n this._addEventListeners()\n\n if (this._config.ride === CLASS_NAME_CAROUSEL) {\n this.cycle()\n }\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n next() {\n this._slide(ORDER_NEXT)\n }\n\n nextWhenVisible() {\n // FIXME TODO use `document.visibilityState`\n // Don't call next when the page isn't visible\n // or the carousel or its parent isn't visible\n if (!document.hidden && isVisible(this._element)) {\n this.next()\n }\n }\n\n prev() {\n this._slide(ORDER_PREV)\n }\n\n pause() {\n if (this._isSliding) {\n triggerTransitionEnd(this._element)\n }\n\n this._clearInterval()\n }\n\n cycle() {\n this._clearInterval()\n this._updateInterval()\n\n this._interval = setInterval(() => this.nextWhenVisible(), this._config.interval)\n }\n\n _maybeEnableCycle() {\n if (!this._config.ride) {\n return\n }\n\n if (this._isSliding) {\n EventHandler.one(this._element, EVENT_SLID, () => this.cycle())\n return\n }\n\n this.cycle()\n }\n\n to(index) {\n const items = this._getItems()\n if (index > items.length - 1 || index < 0) {\n return\n }\n\n if (this._isSliding) {\n EventHandler.one(this._element, EVENT_SLID, () => this.to(index))\n return\n }\n\n const activeIndex = this._getItemIndex(this._getActive())\n if (activeIndex === index) {\n return\n }\n\n const order = index > activeIndex ? ORDER_NEXT : ORDER_PREV\n\n this._slide(order, items[index])\n }\n\n dispose() {\n if (this._swipeHelper) {\n this._swipeHelper.dispose()\n }\n\n super.dispose()\n }\n\n // Private\n _configAfterMerge(config) {\n config.defaultInterval = config.interval\n return config\n }\n\n _addEventListeners() {\n if (this._config.keyboard) {\n EventHandler.on(this._element, EVENT_KEYDOWN, event => this._keydown(event))\n }\n\n if (this._config.pause === 'hover') {\n EventHandler.on(this._element, EVENT_MOUSEENTER, () => this.pause())\n EventHandler.on(this._element, EVENT_MOUSELEAVE, () => this._maybeEnableCycle())\n }\n\n if (this._config.touch && Swipe.isSupported()) {\n this._addTouchEventListeners()\n }\n }\n\n _addTouchEventListeners() {\n for (const img of SelectorEngine.find(SELECTOR_ITEM_IMG, this._element)) {\n EventHandler.on(img, EVENT_DRAG_START, event => event.preventDefault())\n }\n\n const endCallBack = () => {\n if (this._config.pause !== 'hover') {\n return\n }\n\n // If it's a touch-enabled device, mouseenter/leave are fired as\n // part of the mouse compatibility events on first tap - the carousel\n // would stop cycling until user tapped out of it;\n // here, we listen for touchend, explicitly pause the carousel\n // (as if it's the second time we tap on it, mouseenter compat event\n // is NOT fired) and after a timeout (to allow for mouse compatibility\n // events to fire) we explicitly restart cycling\n\n this.pause()\n if (this.touchTimeout) {\n clearTimeout(this.touchTimeout)\n }\n\n this.touchTimeout = setTimeout(() => this._maybeEnableCycle(), TOUCHEVENT_COMPAT_WAIT + this._config.interval)\n }\n\n const swipeConfig = {\n leftCallback: () => this._slide(this._directionToOrder(DIRECTION_LEFT)),\n rightCallback: () => this._slide(this._directionToOrder(DIRECTION_RIGHT)),\n endCallback: endCallBack\n }\n\n this._swipeHelper = new Swipe(this._element, swipeConfig)\n }\n\n _keydown(event) {\n if (/input|textarea/i.test(event.target.tagName)) {\n return\n }\n\n const direction = KEY_TO_DIRECTION[event.key]\n if (direction) {\n event.preventDefault()\n this._slide(this._directionToOrder(direction))\n }\n }\n\n _getItemIndex(element) {\n return this._getItems().indexOf(element)\n }\n\n _setActiveIndicatorElement(index) {\n if (!this._indicatorsElement) {\n return\n }\n\n const activeIndicator = SelectorEngine.findOne(SELECTOR_ACTIVE, this._indicatorsElement)\n\n activeIndicator.classList.remove(CLASS_NAME_ACTIVE)\n activeIndicator.removeAttribute('aria-current')\n\n const newActiveIndicator = SelectorEngine.findOne(`[data-bs-slide-to=\"${index}\"]`, this._indicatorsElement)\n\n if (newActiveIndicator) {\n newActiveIndicator.classList.add(CLASS_NAME_ACTIVE)\n newActiveIndicator.setAttribute('aria-current', 'true')\n }\n }\n\n _updateInterval() {\n const element = this._activeElement || this._getActive()\n\n if (!element) {\n return\n }\n\n const elementInterval = Number.parseInt(element.getAttribute('data-bs-interval'), 10)\n\n this._config.interval = elementInterval || this._config.defaultInterval\n }\n\n _slide(order, element = null) {\n if (this._isSliding) {\n return\n }\n\n const activeElement = this._getActive()\n const isNext = order === ORDER_NEXT\n const nextElement = element || getNextActiveElement(this._getItems(), activeElement, isNext, this._config.wrap)\n\n if (nextElement === activeElement) {\n return\n }\n\n const nextElementIndex = this._getItemIndex(nextElement)\n\n const triggerEvent = eventName => {\n return EventHandler.trigger(this._element, eventName, {\n relatedTarget: nextElement,\n direction: this._orderToDirection(order),\n from: this._getItemIndex(activeElement),\n to: nextElementIndex\n })\n }\n\n const slideEvent = triggerEvent(EVENT_SLIDE)\n\n if (slideEvent.defaultPrevented) {\n return\n }\n\n if (!activeElement || !nextElement) {\n // Some weirdness is happening, so we bail\n // TODO: change tests that use empty divs to avoid this check\n return\n }\n\n const isCycling = Boolean(this._interval)\n this.pause()\n\n this._isSliding = true\n\n this._setActiveIndicatorElement(nextElementIndex)\n this._activeElement = nextElement\n\n const directionalClassName = isNext ? CLASS_NAME_START : CLASS_NAME_END\n const orderClassName = isNext ? CLASS_NAME_NEXT : CLASS_NAME_PREV\n\n nextElement.classList.add(orderClassName)\n\n reflow(nextElement)\n\n activeElement.classList.add(directionalClassName)\n nextElement.classList.add(directionalClassName)\n\n const completeCallBack = () => {\n nextElement.classList.remove(directionalClassName, orderClassName)\n nextElement.classList.add(CLASS_NAME_ACTIVE)\n\n activeElement.classList.remove(CLASS_NAME_ACTIVE, orderClassName, directionalClassName)\n\n this._isSliding = false\n\n triggerEvent(EVENT_SLID)\n }\n\n this._queueCallback(completeCallBack, activeElement, this._isAnimated())\n\n if (isCycling) {\n this.cycle()\n }\n }\n\n _isAnimated() {\n return this._element.classList.contains(CLASS_NAME_SLIDE)\n }\n\n _getActive() {\n return SelectorEngine.findOne(SELECTOR_ACTIVE_ITEM, this._element)\n }\n\n _getItems() {\n return SelectorEngine.find(SELECTOR_ITEM, this._element)\n }\n\n _clearInterval() {\n if (this._interval) {\n clearInterval(this._interval)\n this._interval = null\n }\n }\n\n _directionToOrder(direction) {\n if (isRTL()) {\n return direction === DIRECTION_LEFT ? ORDER_PREV : ORDER_NEXT\n }\n\n return direction === DIRECTION_LEFT ? ORDER_NEXT : ORDER_PREV\n }\n\n _orderToDirection(order) {\n if (isRTL()) {\n return order === ORDER_PREV ? DIRECTION_LEFT : DIRECTION_RIGHT\n }\n\n return order === ORDER_PREV ? DIRECTION_RIGHT : DIRECTION_LEFT\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Carousel.getOrCreateInstance(this, config)\n\n if (typeof config === 'number') {\n data.to(config)\n return\n }\n\n if (typeof config === 'string') {\n if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n }\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_SLIDE, function (event) {\n const target = SelectorEngine.getElementFromSelector(this)\n\n if (!target || !target.classList.contains(CLASS_NAME_CAROUSEL)) {\n return\n }\n\n event.preventDefault()\n\n const carousel = Carousel.getOrCreateInstance(target)\n const slideIndex = this.getAttribute('data-bs-slide-to')\n\n if (slideIndex) {\n carousel.to(slideIndex)\n carousel._maybeEnableCycle()\n return\n }\n\n if (Manipulator.getDataAttribute(this, 'slide') === 'next') {\n carousel.next()\n carousel._maybeEnableCycle()\n return\n }\n\n carousel.prev()\n carousel._maybeEnableCycle()\n})\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n const carousels = SelectorEngine.find(SELECTOR_DATA_RIDE)\n\n for (const carousel of carousels) {\n Carousel.getOrCreateInstance(carousel)\n }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Carousel)\n\nexport default Carousel\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap collapse.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport {\n defineJQueryPlugin,\n getElement,\n reflow\n} from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'collapse'\nconst DATA_KEY = 'bs.collapse'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_COLLAPSE = 'collapse'\nconst CLASS_NAME_COLLAPSING = 'collapsing'\nconst CLASS_NAME_COLLAPSED = 'collapsed'\nconst CLASS_NAME_DEEPER_CHILDREN = `:scope .${CLASS_NAME_COLLAPSE} .${CLASS_NAME_COLLAPSE}`\nconst CLASS_NAME_HORIZONTAL = 'collapse-horizontal'\n\nconst WIDTH = 'width'\nconst HEIGHT = 'height'\n\nconst SELECTOR_ACTIVES = '.collapse.show, .collapse.collapsing'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"collapse\"]'\n\nconst Default = {\n parent: null,\n toggle: true\n}\n\nconst DefaultType = {\n parent: '(null|element)',\n toggle: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Collapse extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._isTransitioning = false\n this._triggerArray = []\n\n const toggleList = SelectorEngine.find(SELECTOR_DATA_TOGGLE)\n\n for (const elem of toggleList) {\n const selector = SelectorEngine.getSelectorFromElement(elem)\n const filterElement = SelectorEngine.find(selector)\n .filter(foundElement => foundElement === this._element)\n\n if (selector !== null && filterElement.length) {\n this._triggerArray.push(elem)\n }\n }\n\n this._initializeChildren()\n\n if (!this._config.parent) {\n this._addAriaAndCollapsedClass(this._triggerArray, this._isShown())\n }\n\n if (this._config.toggle) {\n this.toggle()\n }\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n toggle() {\n if (this._isShown()) {\n this.hide()\n } else {\n this.show()\n }\n }\n\n show() {\n if (this._isTransitioning || this._isShown()) {\n return\n }\n\n let activeChildren = []\n\n // find active children\n if (this._config.parent) {\n activeChildren = this._getFirstLevelChildren(SELECTOR_ACTIVES)\n .filter(element => element !== this._element)\n .map(element => Collapse.getOrCreateInstance(element, { toggle: false }))\n }\n\n if (activeChildren.length && activeChildren[0]._isTransitioning) {\n return\n }\n\n const startEvent = EventHandler.trigger(this._element, EVENT_SHOW)\n if (startEvent.defaultPrevented) {\n return\n }\n\n for (const activeInstance of activeChildren) {\n activeInstance.hide()\n }\n\n const dimension = this._getDimension()\n\n this._element.classList.remove(CLASS_NAME_COLLAPSE)\n this._element.classList.add(CLASS_NAME_COLLAPSING)\n\n this._element.style[dimension] = 0\n\n this._addAriaAndCollapsedClass(this._triggerArray, true)\n this._isTransitioning = true\n\n const complete = () => {\n this._isTransitioning = false\n\n this._element.classList.remove(CLASS_NAME_COLLAPSING)\n this._element.classList.add(CLASS_NAME_COLLAPSE, CLASS_NAME_SHOW)\n\n this._element.style[dimension] = ''\n\n EventHandler.trigger(this._element, EVENT_SHOWN)\n }\n\n const capitalizedDimension = dimension[0].toUpperCase() + dimension.slice(1)\n const scrollSize = `scroll${capitalizedDimension}`\n\n this._queueCallback(complete, this._element, true)\n this._element.style[dimension] = `${this._element[scrollSize]}px`\n }\n\n hide() {\n if (this._isTransitioning || !this._isShown()) {\n return\n }\n\n const startEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n if (startEvent.defaultPrevented) {\n return\n }\n\n const dimension = this._getDimension()\n\n this._element.style[dimension] = `${this._element.getBoundingClientRect()[dimension]}px`\n\n reflow(this._element)\n\n this._element.classList.add(CLASS_NAME_COLLAPSING)\n this._element.classList.remove(CLASS_NAME_COLLAPSE, CLASS_NAME_SHOW)\n\n for (const trigger of this._triggerArray) {\n const element = SelectorEngine.getElementFromSelector(trigger)\n\n if (element && !this._isShown(element)) {\n this._addAriaAndCollapsedClass([trigger], false)\n }\n }\n\n this._isTransitioning = true\n\n const complete = () => {\n this._isTransitioning = false\n this._element.classList.remove(CLASS_NAME_COLLAPSING)\n this._element.classList.add(CLASS_NAME_COLLAPSE)\n EventHandler.trigger(this._element, EVENT_HIDDEN)\n }\n\n this._element.style[dimension] = ''\n\n this._queueCallback(complete, this._element, true)\n }\n\n _isShown(element = this._element) {\n return element.classList.contains(CLASS_NAME_SHOW)\n }\n\n // Private\n _configAfterMerge(config) {\n config.toggle = Boolean(config.toggle) // Coerce string values\n config.parent = getElement(config.parent)\n return config\n }\n\n _getDimension() {\n return this._element.classList.contains(CLASS_NAME_HORIZONTAL) ? WIDTH : HEIGHT\n }\n\n _initializeChildren() {\n if (!this._config.parent) {\n return\n }\n\n const children = this._getFirstLevelChildren(SELECTOR_DATA_TOGGLE)\n\n for (const element of children) {\n const selected = SelectorEngine.getElementFromSelector(element)\n\n if (selected) {\n this._addAriaAndCollapsedClass([element], this._isShown(selected))\n }\n }\n }\n\n _getFirstLevelChildren(selector) {\n const children = SelectorEngine.find(CLASS_NAME_DEEPER_CHILDREN, this._config.parent)\n // remove children if greater depth\n return SelectorEngine.find(selector, this._config.parent).filter(element => !children.includes(element))\n }\n\n _addAriaAndCollapsedClass(triggerArray, isOpen) {\n if (!triggerArray.length) {\n return\n }\n\n for (const element of triggerArray) {\n element.classList.toggle(CLASS_NAME_COLLAPSED, !isOpen)\n element.setAttribute('aria-expanded', isOpen)\n }\n }\n\n // Static\n static jQueryInterface(config) {\n const _config = {}\n if (typeof config === 'string' && /show|hide/.test(config)) {\n _config.toggle = false\n }\n\n return this.each(function () {\n const data = Collapse.getOrCreateInstance(this, _config)\n\n if (typeof config === 'string') {\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n }\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n // preventDefault only for elements (which change the URL) not inside the collapsible element\n if (event.target.tagName === 'A' || (event.delegateTarget && event.delegateTarget.tagName === 'A')) {\n event.preventDefault()\n }\n\n for (const element of SelectorEngine.getMultipleElementsFromSelector(this)) {\n Collapse.getOrCreateInstance(element, { toggle: false }).toggle()\n }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Collapse)\n\nexport default Collapse\n","export var top = 'top';\nexport var bottom = 'bottom';\nexport var right = 'right';\nexport var left = 'left';\nexport var auto = 'auto';\nexport var basePlacements = [top, bottom, right, left];\nexport var start = 'start';\nexport var end = 'end';\nexport var clippingParents = 'clippingParents';\nexport var viewport = 'viewport';\nexport var popper = 'popper';\nexport var reference = 'reference';\nexport var variationPlacements = /*#__PURE__*/basePlacements.reduce(function (acc, placement) {\n return acc.concat([placement + \"-\" + start, placement + \"-\" + end]);\n}, []);\nexport var placements = /*#__PURE__*/[].concat(basePlacements, [auto]).reduce(function (acc, placement) {\n return acc.concat([placement, placement + \"-\" + start, placement + \"-\" + end]);\n}, []); // modifiers that need to read the DOM\n\nexport var beforeRead = 'beforeRead';\nexport var read = 'read';\nexport var afterRead = 'afterRead'; // pure-logic modifiers\n\nexport var beforeMain = 'beforeMain';\nexport var main = 'main';\nexport var afterMain = 'afterMain'; // modifier with the purpose to write to the DOM (or write into a framework state)\n\nexport var beforeWrite = 'beforeWrite';\nexport var write = 'write';\nexport var afterWrite = 'afterWrite';\nexport var modifierPhases = [beforeRead, read, afterRead, beforeMain, main, afterMain, beforeWrite, write, afterWrite];","export default function getNodeName(element) {\n return element ? (element.nodeName || '').toLowerCase() : null;\n}","export default function getWindow(node) {\n if (node == null) {\n return window;\n }\n\n if (node.toString() !== '[object Window]') {\n var ownerDocument = node.ownerDocument;\n return ownerDocument ? ownerDocument.defaultView || window : window;\n }\n\n return node;\n}","import getWindow from \"./getWindow.js\";\n\nfunction isElement(node) {\n var OwnElement = getWindow(node).Element;\n return node instanceof OwnElement || node instanceof Element;\n}\n\nfunction isHTMLElement(node) {\n var OwnElement = getWindow(node).HTMLElement;\n return node instanceof OwnElement || node instanceof HTMLElement;\n}\n\nfunction isShadowRoot(node) {\n // IE 11 has no ShadowRoot\n if (typeof ShadowRoot === 'undefined') {\n return false;\n }\n\n var OwnElement = getWindow(node).ShadowRoot;\n return node instanceof OwnElement || node instanceof ShadowRoot;\n}\n\nexport { isElement, isHTMLElement, isShadowRoot };","import getNodeName from \"../dom-utils/getNodeName.js\";\nimport { isHTMLElement } from \"../dom-utils/instanceOf.js\"; // This modifier takes the styles prepared by the `computeStyles` modifier\n// and applies them to the HTMLElements such as popper and arrow\n\nfunction applyStyles(_ref) {\n var state = _ref.state;\n Object.keys(state.elements).forEach(function (name) {\n var style = state.styles[name] || {};\n var attributes = state.attributes[name] || {};\n var element = state.elements[name]; // arrow is optional + virtual elements\n\n if (!isHTMLElement(element) || !getNodeName(element)) {\n return;\n } // Flow doesn't support to extend this property, but it's the most\n // effective way to apply styles to an HTMLElement\n // $FlowFixMe[cannot-write]\n\n\n Object.assign(element.style, style);\n Object.keys(attributes).forEach(function (name) {\n var value = attributes[name];\n\n if (value === false) {\n element.removeAttribute(name);\n } else {\n element.setAttribute(name, value === true ? '' : value);\n }\n });\n });\n}\n\nfunction effect(_ref2) {\n var state = _ref2.state;\n var initialStyles = {\n popper: {\n position: state.options.strategy,\n left: '0',\n top: '0',\n margin: '0'\n },\n arrow: {\n position: 'absolute'\n },\n reference: {}\n };\n Object.assign(state.elements.popper.style, initialStyles.popper);\n state.styles = initialStyles;\n\n if (state.elements.arrow) {\n Object.assign(state.elements.arrow.style, initialStyles.arrow);\n }\n\n return function () {\n Object.keys(state.elements).forEach(function (name) {\n var element = state.elements[name];\n var attributes = state.attributes[name] || {};\n var styleProperties = Object.keys(state.styles.hasOwnProperty(name) ? state.styles[name] : initialStyles[name]); // Set all values to an empty string to unset them\n\n var style = styleProperties.reduce(function (style, property) {\n style[property] = '';\n return style;\n }, {}); // arrow is optional + virtual elements\n\n if (!isHTMLElement(element) || !getNodeName(element)) {\n return;\n }\n\n Object.assign(element.style, style);\n Object.keys(attributes).forEach(function (attribute) {\n element.removeAttribute(attribute);\n });\n });\n };\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'applyStyles',\n enabled: true,\n phase: 'write',\n fn: applyStyles,\n effect: effect,\n requires: ['computeStyles']\n};","import { auto } from \"../enums.js\";\nexport default function getBasePlacement(placement) {\n return placement.split('-')[0];\n}","export var max = Math.max;\nexport var min = Math.min;\nexport var round = Math.round;","export default function getUAString() {\n var uaData = navigator.userAgentData;\n\n if (uaData != null && uaData.brands && Array.isArray(uaData.brands)) {\n return uaData.brands.map(function (item) {\n return item.brand + \"/\" + item.version;\n }).join(' ');\n }\n\n return navigator.userAgent;\n}","import getUAString from \"../utils/userAgent.js\";\nexport default function isLayoutViewport() {\n return !/^((?!chrome|android).)*safari/i.test(getUAString());\n}","import { isElement, isHTMLElement } from \"./instanceOf.js\";\nimport { round } from \"../utils/math.js\";\nimport getWindow from \"./getWindow.js\";\nimport isLayoutViewport from \"./isLayoutViewport.js\";\nexport default function getBoundingClientRect(element, includeScale, isFixedStrategy) {\n if (includeScale === void 0) {\n includeScale = false;\n }\n\n if (isFixedStrategy === void 0) {\n isFixedStrategy = false;\n }\n\n var clientRect = element.getBoundingClientRect();\n var scaleX = 1;\n var scaleY = 1;\n\n if (includeScale && isHTMLElement(element)) {\n scaleX = element.offsetWidth > 0 ? round(clientRect.width) / element.offsetWidth || 1 : 1;\n scaleY = element.offsetHeight > 0 ? round(clientRect.height) / element.offsetHeight || 1 : 1;\n }\n\n var _ref = isElement(element) ? getWindow(element) : window,\n visualViewport = _ref.visualViewport;\n\n var addVisualOffsets = !isLayoutViewport() && isFixedStrategy;\n var x = (clientRect.left + (addVisualOffsets && visualViewport ? visualViewport.offsetLeft : 0)) / scaleX;\n var y = (clientRect.top + (addVisualOffsets && visualViewport ? visualViewport.offsetTop : 0)) / scaleY;\n var width = clientRect.width / scaleX;\n var height = clientRect.height / scaleY;\n return {\n width: width,\n height: height,\n top: y,\n right: x + width,\n bottom: y + height,\n left: x,\n x: x,\n y: y\n };\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\"; // Returns the layout rect of an element relative to its offsetParent. Layout\n// means it doesn't take into account transforms.\n\nexport default function getLayoutRect(element) {\n var clientRect = getBoundingClientRect(element); // Use the clientRect sizes if it's not been transformed.\n // Fixes https://github.com/popperjs/popper-core/issues/1223\n\n var width = element.offsetWidth;\n var height = element.offsetHeight;\n\n if (Math.abs(clientRect.width - width) <= 1) {\n width = clientRect.width;\n }\n\n if (Math.abs(clientRect.height - height) <= 1) {\n height = clientRect.height;\n }\n\n return {\n x: element.offsetLeft,\n y: element.offsetTop,\n width: width,\n height: height\n };\n}","import { isShadowRoot } from \"./instanceOf.js\";\nexport default function contains(parent, child) {\n var rootNode = child.getRootNode && child.getRootNode(); // First, attempt with faster native method\n\n if (parent.contains(child)) {\n return true;\n } // then fallback to custom implementation with Shadow DOM support\n else if (rootNode && isShadowRoot(rootNode)) {\n var next = child;\n\n do {\n if (next && parent.isSameNode(next)) {\n return true;\n } // $FlowFixMe[prop-missing]: need a better way to handle this...\n\n\n next = next.parentNode || next.host;\n } while (next);\n } // Give up, the result is false\n\n\n return false;\n}","import getWindow from \"./getWindow.js\";\nexport default function getComputedStyle(element) {\n return getWindow(element).getComputedStyle(element);\n}","import getNodeName from \"./getNodeName.js\";\nexport default function isTableElement(element) {\n return ['table', 'td', 'th'].indexOf(getNodeName(element)) >= 0;\n}","import { isElement } from \"./instanceOf.js\";\nexport default function getDocumentElement(element) {\n // $FlowFixMe[incompatible-return]: assume body is always available\n return ((isElement(element) ? element.ownerDocument : // $FlowFixMe[prop-missing]\n element.document) || window.document).documentElement;\n}","import getNodeName from \"./getNodeName.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport { isShadowRoot } from \"./instanceOf.js\";\nexport default function getParentNode(element) {\n if (getNodeName(element) === 'html') {\n return element;\n }\n\n return (// this is a quicker (but less type safe) way to save quite some bytes from the bundle\n // $FlowFixMe[incompatible-return]\n // $FlowFixMe[prop-missing]\n element.assignedSlot || // step into the shadow DOM of the parent of a slotted node\n element.parentNode || ( // DOM Element detected\n isShadowRoot(element) ? element.host : null) || // ShadowRoot detected\n // $FlowFixMe[incompatible-call]: HTMLElement is a Node\n getDocumentElement(element) // fallback\n\n );\n}","import getWindow from \"./getWindow.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport { isHTMLElement, isShadowRoot } from \"./instanceOf.js\";\nimport isTableElement from \"./isTableElement.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport getUAString from \"../utils/userAgent.js\";\n\nfunction getTrueOffsetParent(element) {\n if (!isHTMLElement(element) || // https://github.com/popperjs/popper-core/issues/837\n getComputedStyle(element).position === 'fixed') {\n return null;\n }\n\n return element.offsetParent;\n} // `.offsetParent` reports `null` for fixed elements, while absolute elements\n// return the containing block\n\n\nfunction getContainingBlock(element) {\n var isFirefox = /firefox/i.test(getUAString());\n var isIE = /Trident/i.test(getUAString());\n\n if (isIE && isHTMLElement(element)) {\n // In IE 9, 10 and 11 fixed elements containing block is always established by the viewport\n var elementCss = getComputedStyle(element);\n\n if (elementCss.position === 'fixed') {\n return null;\n }\n }\n\n var currentNode = getParentNode(element);\n\n if (isShadowRoot(currentNode)) {\n currentNode = currentNode.host;\n }\n\n while (isHTMLElement(currentNode) && ['html', 'body'].indexOf(getNodeName(currentNode)) < 0) {\n var css = getComputedStyle(currentNode); // This is non-exhaustive but covers the most common CSS properties that\n // create a containing block.\n // https://developer.mozilla.org/en-US/docs/Web/CSS/Containing_block#identifying_the_containing_block\n\n if (css.transform !== 'none' || css.perspective !== 'none' || css.contain === 'paint' || ['transform', 'perspective'].indexOf(css.willChange) !== -1 || isFirefox && css.willChange === 'filter' || isFirefox && css.filter && css.filter !== 'none') {\n return currentNode;\n } else {\n currentNode = currentNode.parentNode;\n }\n }\n\n return null;\n} // Gets the closest ancestor positioned element. Handles some edge cases,\n// such as table ancestors and cross browser bugs.\n\n\nexport default function getOffsetParent(element) {\n var window = getWindow(element);\n var offsetParent = getTrueOffsetParent(element);\n\n while (offsetParent && isTableElement(offsetParent) && getComputedStyle(offsetParent).position === 'static') {\n offsetParent = getTrueOffsetParent(offsetParent);\n }\n\n if (offsetParent && (getNodeName(offsetParent) === 'html' || getNodeName(offsetParent) === 'body' && getComputedStyle(offsetParent).position === 'static')) {\n return window;\n }\n\n return offsetParent || getContainingBlock(element) || window;\n}","export default function getMainAxisFromPlacement(placement) {\n return ['top', 'bottom'].indexOf(placement) >= 0 ? 'x' : 'y';\n}","import { max as mathMax, min as mathMin } from \"./math.js\";\nexport function within(min, value, max) {\n return mathMax(min, mathMin(value, max));\n}\nexport function withinMaxClamp(min, value, max) {\n var v = within(min, value, max);\n return v > max ? max : v;\n}","import getFreshSideObject from \"./getFreshSideObject.js\";\nexport default function mergePaddingObject(paddingObject) {\n return Object.assign({}, getFreshSideObject(), paddingObject);\n}","export default function getFreshSideObject() {\n return {\n top: 0,\n right: 0,\n bottom: 0,\n left: 0\n };\n}","export default function expandToHashMap(value, keys) {\n return keys.reduce(function (hashMap, key) {\n hashMap[key] = value;\n return hashMap;\n }, {});\n}","import getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getLayoutRect from \"../dom-utils/getLayoutRect.js\";\nimport contains from \"../dom-utils/contains.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport getMainAxisFromPlacement from \"../utils/getMainAxisFromPlacement.js\";\nimport { within } from \"../utils/within.js\";\nimport mergePaddingObject from \"../utils/mergePaddingObject.js\";\nimport expandToHashMap from \"../utils/expandToHashMap.js\";\nimport { left, right, basePlacements, top, bottom } from \"../enums.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar toPaddingObject = function toPaddingObject(padding, state) {\n padding = typeof padding === 'function' ? padding(Object.assign({}, state.rects, {\n placement: state.placement\n })) : padding;\n return mergePaddingObject(typeof padding !== 'number' ? padding : expandToHashMap(padding, basePlacements));\n};\n\nfunction arrow(_ref) {\n var _state$modifiersData$;\n\n var state = _ref.state,\n name = _ref.name,\n options = _ref.options;\n var arrowElement = state.elements.arrow;\n var popperOffsets = state.modifiersData.popperOffsets;\n var basePlacement = getBasePlacement(state.placement);\n var axis = getMainAxisFromPlacement(basePlacement);\n var isVertical = [left, right].indexOf(basePlacement) >= 0;\n var len = isVertical ? 'height' : 'width';\n\n if (!arrowElement || !popperOffsets) {\n return;\n }\n\n var paddingObject = toPaddingObject(options.padding, state);\n var arrowRect = getLayoutRect(arrowElement);\n var minProp = axis === 'y' ? top : left;\n var maxProp = axis === 'y' ? bottom : right;\n var endDiff = state.rects.reference[len] + state.rects.reference[axis] - popperOffsets[axis] - state.rects.popper[len];\n var startDiff = popperOffsets[axis] - state.rects.reference[axis];\n var arrowOffsetParent = getOffsetParent(arrowElement);\n var clientSize = arrowOffsetParent ? axis === 'y' ? arrowOffsetParent.clientHeight || 0 : arrowOffsetParent.clientWidth || 0 : 0;\n var centerToReference = endDiff / 2 - startDiff / 2; // Make sure the arrow doesn't overflow the popper if the center point is\n // outside of the popper bounds\n\n var min = paddingObject[minProp];\n var max = clientSize - arrowRect[len] - paddingObject[maxProp];\n var center = clientSize / 2 - arrowRect[len] / 2 + centerToReference;\n var offset = within(min, center, max); // Prevents breaking syntax highlighting...\n\n var axisProp = axis;\n state.modifiersData[name] = (_state$modifiersData$ = {}, _state$modifiersData$[axisProp] = offset, _state$modifiersData$.centerOffset = offset - center, _state$modifiersData$);\n}\n\nfunction effect(_ref2) {\n var state = _ref2.state,\n options = _ref2.options;\n var _options$element = options.element,\n arrowElement = _options$element === void 0 ? '[data-popper-arrow]' : _options$element;\n\n if (arrowElement == null) {\n return;\n } // CSS selector\n\n\n if (typeof arrowElement === 'string') {\n arrowElement = state.elements.popper.querySelector(arrowElement);\n\n if (!arrowElement) {\n return;\n }\n }\n\n if (!contains(state.elements.popper, arrowElement)) {\n return;\n }\n\n state.elements.arrow = arrowElement;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'arrow',\n enabled: true,\n phase: 'main',\n fn: arrow,\n effect: effect,\n requires: ['popperOffsets'],\n requiresIfExists: ['preventOverflow']\n};","export default function getVariation(placement) {\n return placement.split('-')[1];\n}","import { top, left, right, bottom, end } from \"../enums.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport getWindow from \"../dom-utils/getWindow.js\";\nimport getDocumentElement from \"../dom-utils/getDocumentElement.js\";\nimport getComputedStyle from \"../dom-utils/getComputedStyle.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getVariation from \"../utils/getVariation.js\";\nimport { round } from \"../utils/math.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar unsetSides = {\n top: 'auto',\n right: 'auto',\n bottom: 'auto',\n left: 'auto'\n}; // Round the offsets to the nearest suitable subpixel based on the DPR.\n// Zooming can change the DPR, but it seems to report a value that will\n// cleanly divide the values into the appropriate subpixels.\n\nfunction roundOffsetsByDPR(_ref, win) {\n var x = _ref.x,\n y = _ref.y;\n var dpr = win.devicePixelRatio || 1;\n return {\n x: round(x * dpr) / dpr || 0,\n y: round(y * dpr) / dpr || 0\n };\n}\n\nexport function mapToStyles(_ref2) {\n var _Object$assign2;\n\n var popper = _ref2.popper,\n popperRect = _ref2.popperRect,\n placement = _ref2.placement,\n variation = _ref2.variation,\n offsets = _ref2.offsets,\n position = _ref2.position,\n gpuAcceleration = _ref2.gpuAcceleration,\n adaptive = _ref2.adaptive,\n roundOffsets = _ref2.roundOffsets,\n isFixed = _ref2.isFixed;\n var _offsets$x = offsets.x,\n x = _offsets$x === void 0 ? 0 : _offsets$x,\n _offsets$y = offsets.y,\n y = _offsets$y === void 0 ? 0 : _offsets$y;\n\n var _ref3 = typeof roundOffsets === 'function' ? roundOffsets({\n x: x,\n y: y\n }) : {\n x: x,\n y: y\n };\n\n x = _ref3.x;\n y = _ref3.y;\n var hasX = offsets.hasOwnProperty('x');\n var hasY = offsets.hasOwnProperty('y');\n var sideX = left;\n var sideY = top;\n var win = window;\n\n if (adaptive) {\n var offsetParent = getOffsetParent(popper);\n var heightProp = 'clientHeight';\n var widthProp = 'clientWidth';\n\n if (offsetParent === getWindow(popper)) {\n offsetParent = getDocumentElement(popper);\n\n if (getComputedStyle(offsetParent).position !== 'static' && position === 'absolute') {\n heightProp = 'scrollHeight';\n widthProp = 'scrollWidth';\n }\n } // $FlowFixMe[incompatible-cast]: force type refinement, we compare offsetParent with window above, but Flow doesn't detect it\n\n\n offsetParent = offsetParent;\n\n if (placement === top || (placement === left || placement === right) && variation === end) {\n sideY = bottom;\n var offsetY = isFixed && offsetParent === win && win.visualViewport ? win.visualViewport.height : // $FlowFixMe[prop-missing]\n offsetParent[heightProp];\n y -= offsetY - popperRect.height;\n y *= gpuAcceleration ? 1 : -1;\n }\n\n if (placement === left || (placement === top || placement === bottom) && variation === end) {\n sideX = right;\n var offsetX = isFixed && offsetParent === win && win.visualViewport ? win.visualViewport.width : // $FlowFixMe[prop-missing]\n offsetParent[widthProp];\n x -= offsetX - popperRect.width;\n x *= gpuAcceleration ? 1 : -1;\n }\n }\n\n var commonStyles = Object.assign({\n position: position\n }, adaptive && unsetSides);\n\n var _ref4 = roundOffsets === true ? roundOffsetsByDPR({\n x: x,\n y: y\n }, getWindow(popper)) : {\n x: x,\n y: y\n };\n\n x = _ref4.x;\n y = _ref4.y;\n\n if (gpuAcceleration) {\n var _Object$assign;\n\n return Object.assign({}, commonStyles, (_Object$assign = {}, _Object$assign[sideY] = hasY ? '0' : '', _Object$assign[sideX] = hasX ? '0' : '', _Object$assign.transform = (win.devicePixelRatio || 1) <= 1 ? \"translate(\" + x + \"px, \" + y + \"px)\" : \"translate3d(\" + x + \"px, \" + y + \"px, 0)\", _Object$assign));\n }\n\n return Object.assign({}, commonStyles, (_Object$assign2 = {}, _Object$assign2[sideY] = hasY ? y + \"px\" : '', _Object$assign2[sideX] = hasX ? x + \"px\" : '', _Object$assign2.transform = '', _Object$assign2));\n}\n\nfunction computeStyles(_ref5) {\n var state = _ref5.state,\n options = _ref5.options;\n var _options$gpuAccelerat = options.gpuAcceleration,\n gpuAcceleration = _options$gpuAccelerat === void 0 ? true : _options$gpuAccelerat,\n _options$adaptive = options.adaptive,\n adaptive = _options$adaptive === void 0 ? true : _options$adaptive,\n _options$roundOffsets = options.roundOffsets,\n roundOffsets = _options$roundOffsets === void 0 ? true : _options$roundOffsets;\n var commonStyles = {\n placement: getBasePlacement(state.placement),\n variation: getVariation(state.placement),\n popper: state.elements.popper,\n popperRect: state.rects.popper,\n gpuAcceleration: gpuAcceleration,\n isFixed: state.options.strategy === 'fixed'\n };\n\n if (state.modifiersData.popperOffsets != null) {\n state.styles.popper = Object.assign({}, state.styles.popper, mapToStyles(Object.assign({}, commonStyles, {\n offsets: state.modifiersData.popperOffsets,\n position: state.options.strategy,\n adaptive: adaptive,\n roundOffsets: roundOffsets\n })));\n }\n\n if (state.modifiersData.arrow != null) {\n state.styles.arrow = Object.assign({}, state.styles.arrow, mapToStyles(Object.assign({}, commonStyles, {\n offsets: state.modifiersData.arrow,\n position: 'absolute',\n adaptive: false,\n roundOffsets: roundOffsets\n })));\n }\n\n state.attributes.popper = Object.assign({}, state.attributes.popper, {\n 'data-popper-placement': state.placement\n });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'computeStyles',\n enabled: true,\n phase: 'beforeWrite',\n fn: computeStyles,\n data: {}\n};","import getWindow from \"../dom-utils/getWindow.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar passive = {\n passive: true\n};\n\nfunction effect(_ref) {\n var state = _ref.state,\n instance = _ref.instance,\n options = _ref.options;\n var _options$scroll = options.scroll,\n scroll = _options$scroll === void 0 ? true : _options$scroll,\n _options$resize = options.resize,\n resize = _options$resize === void 0 ? true : _options$resize;\n var window = getWindow(state.elements.popper);\n var scrollParents = [].concat(state.scrollParents.reference, state.scrollParents.popper);\n\n if (scroll) {\n scrollParents.forEach(function (scrollParent) {\n scrollParent.addEventListener('scroll', instance.update, passive);\n });\n }\n\n if (resize) {\n window.addEventListener('resize', instance.update, passive);\n }\n\n return function () {\n if (scroll) {\n scrollParents.forEach(function (scrollParent) {\n scrollParent.removeEventListener('scroll', instance.update, passive);\n });\n }\n\n if (resize) {\n window.removeEventListener('resize', instance.update, passive);\n }\n };\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'eventListeners',\n enabled: true,\n phase: 'write',\n fn: function fn() {},\n effect: effect,\n data: {}\n};","var hash = {\n left: 'right',\n right: 'left',\n bottom: 'top',\n top: 'bottom'\n};\nexport default function getOppositePlacement(placement) {\n return placement.replace(/left|right|bottom|top/g, function (matched) {\n return hash[matched];\n });\n}","var hash = {\n start: 'end',\n end: 'start'\n};\nexport default function getOppositeVariationPlacement(placement) {\n return placement.replace(/start|end/g, function (matched) {\n return hash[matched];\n });\n}","import getWindow from \"./getWindow.js\";\nexport default function getWindowScroll(node) {\n var win = getWindow(node);\n var scrollLeft = win.pageXOffset;\n var scrollTop = win.pageYOffset;\n return {\n scrollLeft: scrollLeft,\n scrollTop: scrollTop\n };\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getWindowScroll from \"./getWindowScroll.js\";\nexport default function getWindowScrollBarX(element) {\n // If has a CSS width greater than the viewport, then this will be\n // incorrect for RTL.\n // Popper 1 is broken in this case and never had a bug report so let's assume\n // it's not an issue. I don't think anyone ever specifies width on \n // anyway.\n // Browsers where the left scrollbar doesn't cause an issue report `0` for\n // this (e.g. Edge 2019, IE11, Safari)\n return getBoundingClientRect(getDocumentElement(element)).left + getWindowScroll(element).scrollLeft;\n}","import getComputedStyle from \"./getComputedStyle.js\";\nexport default function isScrollParent(element) {\n // Firefox wants us to check `-x` and `-y` variations as well\n var _getComputedStyle = getComputedStyle(element),\n overflow = _getComputedStyle.overflow,\n overflowX = _getComputedStyle.overflowX,\n overflowY = _getComputedStyle.overflowY;\n\n return /auto|scroll|overlay|hidden/.test(overflow + overflowY + overflowX);\n}","import getParentNode from \"./getParentNode.js\";\nimport isScrollParent from \"./isScrollParent.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nexport default function getScrollParent(node) {\n if (['html', 'body', '#document'].indexOf(getNodeName(node)) >= 0) {\n // $FlowFixMe[incompatible-return]: assume body is always available\n return node.ownerDocument.body;\n }\n\n if (isHTMLElement(node) && isScrollParent(node)) {\n return node;\n }\n\n return getScrollParent(getParentNode(node));\n}","import getScrollParent from \"./getScrollParent.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport getWindow from \"./getWindow.js\";\nimport isScrollParent from \"./isScrollParent.js\";\n/*\ngiven a DOM element, return the list of all scroll parents, up the list of ancesors\nuntil we get to the top window object. This list is what we attach scroll listeners\nto, because if any of these parent elements scroll, we'll need to re-calculate the\nreference element's position.\n*/\n\nexport default function listScrollParents(element, list) {\n var _element$ownerDocumen;\n\n if (list === void 0) {\n list = [];\n }\n\n var scrollParent = getScrollParent(element);\n var isBody = scrollParent === ((_element$ownerDocumen = element.ownerDocument) == null ? void 0 : _element$ownerDocumen.body);\n var win = getWindow(scrollParent);\n var target = isBody ? [win].concat(win.visualViewport || [], isScrollParent(scrollParent) ? scrollParent : []) : scrollParent;\n var updatedList = list.concat(target);\n return isBody ? updatedList : // $FlowFixMe[incompatible-call]: isBody tells us target will be an HTMLElement here\n updatedList.concat(listScrollParents(getParentNode(target)));\n}","export default function rectToClientRect(rect) {\n return Object.assign({}, rect, {\n left: rect.x,\n top: rect.y,\n right: rect.x + rect.width,\n bottom: rect.y + rect.height\n });\n}","import { viewport } from \"../enums.js\";\nimport getViewportRect from \"./getViewportRect.js\";\nimport getDocumentRect from \"./getDocumentRect.js\";\nimport listScrollParents from \"./listScrollParents.js\";\nimport getOffsetParent from \"./getOffsetParent.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport { isElement, isHTMLElement } from \"./instanceOf.js\";\nimport getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport contains from \"./contains.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport rectToClientRect from \"../utils/rectToClientRect.js\";\nimport { max, min } from \"../utils/math.js\";\n\nfunction getInnerBoundingClientRect(element, strategy) {\n var rect = getBoundingClientRect(element, false, strategy === 'fixed');\n rect.top = rect.top + element.clientTop;\n rect.left = rect.left + element.clientLeft;\n rect.bottom = rect.top + element.clientHeight;\n rect.right = rect.left + element.clientWidth;\n rect.width = element.clientWidth;\n rect.height = element.clientHeight;\n rect.x = rect.left;\n rect.y = rect.top;\n return rect;\n}\n\nfunction getClientRectFromMixedType(element, clippingParent, strategy) {\n return clippingParent === viewport ? rectToClientRect(getViewportRect(element, strategy)) : isElement(clippingParent) ? getInnerBoundingClientRect(clippingParent, strategy) : rectToClientRect(getDocumentRect(getDocumentElement(element)));\n} // A \"clipping parent\" is an overflowable container with the characteristic of\n// clipping (or hiding) overflowing elements with a position different from\n// `initial`\n\n\nfunction getClippingParents(element) {\n var clippingParents = listScrollParents(getParentNode(element));\n var canEscapeClipping = ['absolute', 'fixed'].indexOf(getComputedStyle(element).position) >= 0;\n var clipperElement = canEscapeClipping && isHTMLElement(element) ? getOffsetParent(element) : element;\n\n if (!isElement(clipperElement)) {\n return [];\n } // $FlowFixMe[incompatible-return]: https://github.com/facebook/flow/issues/1414\n\n\n return clippingParents.filter(function (clippingParent) {\n return isElement(clippingParent) && contains(clippingParent, clipperElement) && getNodeName(clippingParent) !== 'body';\n });\n} // Gets the maximum area that the element is visible in due to any number of\n// clipping parents\n\n\nexport default function getClippingRect(element, boundary, rootBoundary, strategy) {\n var mainClippingParents = boundary === 'clippingParents' ? getClippingParents(element) : [].concat(boundary);\n var clippingParents = [].concat(mainClippingParents, [rootBoundary]);\n var firstClippingParent = clippingParents[0];\n var clippingRect = clippingParents.reduce(function (accRect, clippingParent) {\n var rect = getClientRectFromMixedType(element, clippingParent, strategy);\n accRect.top = max(rect.top, accRect.top);\n accRect.right = min(rect.right, accRect.right);\n accRect.bottom = min(rect.bottom, accRect.bottom);\n accRect.left = max(rect.left, accRect.left);\n return accRect;\n }, getClientRectFromMixedType(element, firstClippingParent, strategy));\n clippingRect.width = clippingRect.right - clippingRect.left;\n clippingRect.height = clippingRect.bottom - clippingRect.top;\n clippingRect.x = clippingRect.left;\n clippingRect.y = clippingRect.top;\n return clippingRect;\n}","import getWindow from \"./getWindow.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport isLayoutViewport from \"./isLayoutViewport.js\";\nexport default function getViewportRect(element, strategy) {\n var win = getWindow(element);\n var html = getDocumentElement(element);\n var visualViewport = win.visualViewport;\n var width = html.clientWidth;\n var height = html.clientHeight;\n var x = 0;\n var y = 0;\n\n if (visualViewport) {\n width = visualViewport.width;\n height = visualViewport.height;\n var layoutViewport = isLayoutViewport();\n\n if (layoutViewport || !layoutViewport && strategy === 'fixed') {\n x = visualViewport.offsetLeft;\n y = visualViewport.offsetTop;\n }\n }\n\n return {\n width: width,\n height: height,\n x: x + getWindowScrollBarX(element),\n y: y\n };\n}","import getDocumentElement from \"./getDocumentElement.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport getWindowScroll from \"./getWindowScroll.js\";\nimport { max } from \"../utils/math.js\"; // Gets the entire size of the scrollable document area, even extending outside\n// of the `` and `` rect bounds if horizontally scrollable\n\nexport default function getDocumentRect(element) {\n var _element$ownerDocumen;\n\n var html = getDocumentElement(element);\n var winScroll = getWindowScroll(element);\n var body = (_element$ownerDocumen = element.ownerDocument) == null ? void 0 : _element$ownerDocumen.body;\n var width = max(html.scrollWidth, html.clientWidth, body ? body.scrollWidth : 0, body ? body.clientWidth : 0);\n var height = max(html.scrollHeight, html.clientHeight, body ? body.scrollHeight : 0, body ? body.clientHeight : 0);\n var x = -winScroll.scrollLeft + getWindowScrollBarX(element);\n var y = -winScroll.scrollTop;\n\n if (getComputedStyle(body || html).direction === 'rtl') {\n x += max(html.clientWidth, body ? body.clientWidth : 0) - width;\n }\n\n return {\n width: width,\n height: height,\n x: x,\n y: y\n };\n}","import getBasePlacement from \"./getBasePlacement.js\";\nimport getVariation from \"./getVariation.js\";\nimport getMainAxisFromPlacement from \"./getMainAxisFromPlacement.js\";\nimport { top, right, bottom, left, start, end } from \"../enums.js\";\nexport default function computeOffsets(_ref) {\n var reference = _ref.reference,\n element = _ref.element,\n placement = _ref.placement;\n var basePlacement = placement ? getBasePlacement(placement) : null;\n var variation = placement ? getVariation(placement) : null;\n var commonX = reference.x + reference.width / 2 - element.width / 2;\n var commonY = reference.y + reference.height / 2 - element.height / 2;\n var offsets;\n\n switch (basePlacement) {\n case top:\n offsets = {\n x: commonX,\n y: reference.y - element.height\n };\n break;\n\n case bottom:\n offsets = {\n x: commonX,\n y: reference.y + reference.height\n };\n break;\n\n case right:\n offsets = {\n x: reference.x + reference.width,\n y: commonY\n };\n break;\n\n case left:\n offsets = {\n x: reference.x - element.width,\n y: commonY\n };\n break;\n\n default:\n offsets = {\n x: reference.x,\n y: reference.y\n };\n }\n\n var mainAxis = basePlacement ? getMainAxisFromPlacement(basePlacement) : null;\n\n if (mainAxis != null) {\n var len = mainAxis === 'y' ? 'height' : 'width';\n\n switch (variation) {\n case start:\n offsets[mainAxis] = offsets[mainAxis] - (reference[len] / 2 - element[len] / 2);\n break;\n\n case end:\n offsets[mainAxis] = offsets[mainAxis] + (reference[len] / 2 - element[len] / 2);\n break;\n\n default:\n }\n }\n\n return offsets;\n}","import getClippingRect from \"../dom-utils/getClippingRect.js\";\nimport getDocumentElement from \"../dom-utils/getDocumentElement.js\";\nimport getBoundingClientRect from \"../dom-utils/getBoundingClientRect.js\";\nimport computeOffsets from \"./computeOffsets.js\";\nimport rectToClientRect from \"./rectToClientRect.js\";\nimport { clippingParents, reference, popper, bottom, top, right, basePlacements, viewport } from \"../enums.js\";\nimport { isElement } from \"../dom-utils/instanceOf.js\";\nimport mergePaddingObject from \"./mergePaddingObject.js\";\nimport expandToHashMap from \"./expandToHashMap.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport default function detectOverflow(state, options) {\n if (options === void 0) {\n options = {};\n }\n\n var _options = options,\n _options$placement = _options.placement,\n placement = _options$placement === void 0 ? state.placement : _options$placement,\n _options$strategy = _options.strategy,\n strategy = _options$strategy === void 0 ? state.strategy : _options$strategy,\n _options$boundary = _options.boundary,\n boundary = _options$boundary === void 0 ? clippingParents : _options$boundary,\n _options$rootBoundary = _options.rootBoundary,\n rootBoundary = _options$rootBoundary === void 0 ? viewport : _options$rootBoundary,\n _options$elementConte = _options.elementContext,\n elementContext = _options$elementConte === void 0 ? popper : _options$elementConte,\n _options$altBoundary = _options.altBoundary,\n altBoundary = _options$altBoundary === void 0 ? false : _options$altBoundary,\n _options$padding = _options.padding,\n padding = _options$padding === void 0 ? 0 : _options$padding;\n var paddingObject = mergePaddingObject(typeof padding !== 'number' ? padding : expandToHashMap(padding, basePlacements));\n var altContext = elementContext === popper ? reference : popper;\n var popperRect = state.rects.popper;\n var element = state.elements[altBoundary ? altContext : elementContext];\n var clippingClientRect = getClippingRect(isElement(element) ? element : element.contextElement || getDocumentElement(state.elements.popper), boundary, rootBoundary, strategy);\n var referenceClientRect = getBoundingClientRect(state.elements.reference);\n var popperOffsets = computeOffsets({\n reference: referenceClientRect,\n element: popperRect,\n strategy: 'absolute',\n placement: placement\n });\n var popperClientRect = rectToClientRect(Object.assign({}, popperRect, popperOffsets));\n var elementClientRect = elementContext === popper ? popperClientRect : referenceClientRect; // positive = overflowing the clipping rect\n // 0 or negative = within the clipping rect\n\n var overflowOffsets = {\n top: clippingClientRect.top - elementClientRect.top + paddingObject.top,\n bottom: elementClientRect.bottom - clippingClientRect.bottom + paddingObject.bottom,\n left: clippingClientRect.left - elementClientRect.left + paddingObject.left,\n right: elementClientRect.right - clippingClientRect.right + paddingObject.right\n };\n var offsetData = state.modifiersData.offset; // Offsets can be applied only to the popper element\n\n if (elementContext === popper && offsetData) {\n var offset = offsetData[placement];\n Object.keys(overflowOffsets).forEach(function (key) {\n var multiply = [right, bottom].indexOf(key) >= 0 ? 1 : -1;\n var axis = [top, bottom].indexOf(key) >= 0 ? 'y' : 'x';\n overflowOffsets[key] += offset[axis] * multiply;\n });\n }\n\n return overflowOffsets;\n}","import getVariation from \"./getVariation.js\";\nimport { variationPlacements, basePlacements, placements as allPlacements } from \"../enums.js\";\nimport detectOverflow from \"./detectOverflow.js\";\nimport getBasePlacement from \"./getBasePlacement.js\";\nexport default function computeAutoPlacement(state, options) {\n if (options === void 0) {\n options = {};\n }\n\n var _options = options,\n placement = _options.placement,\n boundary = _options.boundary,\n rootBoundary = _options.rootBoundary,\n padding = _options.padding,\n flipVariations = _options.flipVariations,\n _options$allowedAutoP = _options.allowedAutoPlacements,\n allowedAutoPlacements = _options$allowedAutoP === void 0 ? allPlacements : _options$allowedAutoP;\n var variation = getVariation(placement);\n var placements = variation ? flipVariations ? variationPlacements : variationPlacements.filter(function (placement) {\n return getVariation(placement) === variation;\n }) : basePlacements;\n var allowedPlacements = placements.filter(function (placement) {\n return allowedAutoPlacements.indexOf(placement) >= 0;\n });\n\n if (allowedPlacements.length === 0) {\n allowedPlacements = placements;\n } // $FlowFixMe[incompatible-type]: Flow seems to have problems with two array unions...\n\n\n var overflows = allowedPlacements.reduce(function (acc, placement) {\n acc[placement] = detectOverflow(state, {\n placement: placement,\n boundary: boundary,\n rootBoundary: rootBoundary,\n padding: padding\n })[getBasePlacement(placement)];\n return acc;\n }, {});\n return Object.keys(overflows).sort(function (a, b) {\n return overflows[a] - overflows[b];\n });\n}","import getOppositePlacement from \"../utils/getOppositePlacement.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getOppositeVariationPlacement from \"../utils/getOppositeVariationPlacement.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\nimport computeAutoPlacement from \"../utils/computeAutoPlacement.js\";\nimport { bottom, top, start, right, left, auto } from \"../enums.js\";\nimport getVariation from \"../utils/getVariation.js\"; // eslint-disable-next-line import/no-unused-modules\n\nfunction getExpandedFallbackPlacements(placement) {\n if (getBasePlacement(placement) === auto) {\n return [];\n }\n\n var oppositePlacement = getOppositePlacement(placement);\n return [getOppositeVariationPlacement(placement), oppositePlacement, getOppositeVariationPlacement(oppositePlacement)];\n}\n\nfunction flip(_ref) {\n var state = _ref.state,\n options = _ref.options,\n name = _ref.name;\n\n if (state.modifiersData[name]._skip) {\n return;\n }\n\n var _options$mainAxis = options.mainAxis,\n checkMainAxis = _options$mainAxis === void 0 ? true : _options$mainAxis,\n _options$altAxis = options.altAxis,\n checkAltAxis = _options$altAxis === void 0 ? true : _options$altAxis,\n specifiedFallbackPlacements = options.fallbackPlacements,\n padding = options.padding,\n boundary = options.boundary,\n rootBoundary = options.rootBoundary,\n altBoundary = options.altBoundary,\n _options$flipVariatio = options.flipVariations,\n flipVariations = _options$flipVariatio === void 0 ? true : _options$flipVariatio,\n allowedAutoPlacements = options.allowedAutoPlacements;\n var preferredPlacement = state.options.placement;\n var basePlacement = getBasePlacement(preferredPlacement);\n var isBasePlacement = basePlacement === preferredPlacement;\n var fallbackPlacements = specifiedFallbackPlacements || (isBasePlacement || !flipVariations ? [getOppositePlacement(preferredPlacement)] : getExpandedFallbackPlacements(preferredPlacement));\n var placements = [preferredPlacement].concat(fallbackPlacements).reduce(function (acc, placement) {\n return acc.concat(getBasePlacement(placement) === auto ? computeAutoPlacement(state, {\n placement: placement,\n boundary: boundary,\n rootBoundary: rootBoundary,\n padding: padding,\n flipVariations: flipVariations,\n allowedAutoPlacements: allowedAutoPlacements\n }) : placement);\n }, []);\n var referenceRect = state.rects.reference;\n var popperRect = state.rects.popper;\n var checksMap = new Map();\n var makeFallbackChecks = true;\n var firstFittingPlacement = placements[0];\n\n for (var i = 0; i < placements.length; i++) {\n var placement = placements[i];\n\n var _basePlacement = getBasePlacement(placement);\n\n var isStartVariation = getVariation(placement) === start;\n var isVertical = [top, bottom].indexOf(_basePlacement) >= 0;\n var len = isVertical ? 'width' : 'height';\n var overflow = detectOverflow(state, {\n placement: placement,\n boundary: boundary,\n rootBoundary: rootBoundary,\n altBoundary: altBoundary,\n padding: padding\n });\n var mainVariationSide = isVertical ? isStartVariation ? right : left : isStartVariation ? bottom : top;\n\n if (referenceRect[len] > popperRect[len]) {\n mainVariationSide = getOppositePlacement(mainVariationSide);\n }\n\n var altVariationSide = getOppositePlacement(mainVariationSide);\n var checks = [];\n\n if (checkMainAxis) {\n checks.push(overflow[_basePlacement] <= 0);\n }\n\n if (checkAltAxis) {\n checks.push(overflow[mainVariationSide] <= 0, overflow[altVariationSide] <= 0);\n }\n\n if (checks.every(function (check) {\n return check;\n })) {\n firstFittingPlacement = placement;\n makeFallbackChecks = false;\n break;\n }\n\n checksMap.set(placement, checks);\n }\n\n if (makeFallbackChecks) {\n // `2` may be desired in some cases – research later\n var numberOfChecks = flipVariations ? 3 : 1;\n\n var _loop = function _loop(_i) {\n var fittingPlacement = placements.find(function (placement) {\n var checks = checksMap.get(placement);\n\n if (checks) {\n return checks.slice(0, _i).every(function (check) {\n return check;\n });\n }\n });\n\n if (fittingPlacement) {\n firstFittingPlacement = fittingPlacement;\n return \"break\";\n }\n };\n\n for (var _i = numberOfChecks; _i > 0; _i--) {\n var _ret = _loop(_i);\n\n if (_ret === \"break\") break;\n }\n }\n\n if (state.placement !== firstFittingPlacement) {\n state.modifiersData[name]._skip = true;\n state.placement = firstFittingPlacement;\n state.reset = true;\n }\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'flip',\n enabled: true,\n phase: 'main',\n fn: flip,\n requiresIfExists: ['offset'],\n data: {\n _skip: false\n }\n};","import { top, bottom, left, right } from \"../enums.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\n\nfunction getSideOffsets(overflow, rect, preventedOffsets) {\n if (preventedOffsets === void 0) {\n preventedOffsets = {\n x: 0,\n y: 0\n };\n }\n\n return {\n top: overflow.top - rect.height - preventedOffsets.y,\n right: overflow.right - rect.width + preventedOffsets.x,\n bottom: overflow.bottom - rect.height + preventedOffsets.y,\n left: overflow.left - rect.width - preventedOffsets.x\n };\n}\n\nfunction isAnySideFullyClipped(overflow) {\n return [top, right, bottom, left].some(function (side) {\n return overflow[side] >= 0;\n });\n}\n\nfunction hide(_ref) {\n var state = _ref.state,\n name = _ref.name;\n var referenceRect = state.rects.reference;\n var popperRect = state.rects.popper;\n var preventedOffsets = state.modifiersData.preventOverflow;\n var referenceOverflow = detectOverflow(state, {\n elementContext: 'reference'\n });\n var popperAltOverflow = detectOverflow(state, {\n altBoundary: true\n });\n var referenceClippingOffsets = getSideOffsets(referenceOverflow, referenceRect);\n var popperEscapeOffsets = getSideOffsets(popperAltOverflow, popperRect, preventedOffsets);\n var isReferenceHidden = isAnySideFullyClipped(referenceClippingOffsets);\n var hasPopperEscaped = isAnySideFullyClipped(popperEscapeOffsets);\n state.modifiersData[name] = {\n referenceClippingOffsets: referenceClippingOffsets,\n popperEscapeOffsets: popperEscapeOffsets,\n isReferenceHidden: isReferenceHidden,\n hasPopperEscaped: hasPopperEscaped\n };\n state.attributes.popper = Object.assign({}, state.attributes.popper, {\n 'data-popper-reference-hidden': isReferenceHidden,\n 'data-popper-escaped': hasPopperEscaped\n });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'hide',\n enabled: true,\n phase: 'main',\n requiresIfExists: ['preventOverflow'],\n fn: hide\n};","import getBasePlacement from \"../utils/getBasePlacement.js\";\nimport { top, left, right, placements } from \"../enums.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport function distanceAndSkiddingToXY(placement, rects, offset) {\n var basePlacement = getBasePlacement(placement);\n var invertDistance = [left, top].indexOf(basePlacement) >= 0 ? -1 : 1;\n\n var _ref = typeof offset === 'function' ? offset(Object.assign({}, rects, {\n placement: placement\n })) : offset,\n skidding = _ref[0],\n distance = _ref[1];\n\n skidding = skidding || 0;\n distance = (distance || 0) * invertDistance;\n return [left, right].indexOf(basePlacement) >= 0 ? {\n x: distance,\n y: skidding\n } : {\n x: skidding,\n y: distance\n };\n}\n\nfunction offset(_ref2) {\n var state = _ref2.state,\n options = _ref2.options,\n name = _ref2.name;\n var _options$offset = options.offset,\n offset = _options$offset === void 0 ? [0, 0] : _options$offset;\n var data = placements.reduce(function (acc, placement) {\n acc[placement] = distanceAndSkiddingToXY(placement, state.rects, offset);\n return acc;\n }, {});\n var _data$state$placement = data[state.placement],\n x = _data$state$placement.x,\n y = _data$state$placement.y;\n\n if (state.modifiersData.popperOffsets != null) {\n state.modifiersData.popperOffsets.x += x;\n state.modifiersData.popperOffsets.y += y;\n }\n\n state.modifiersData[name] = data;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'offset',\n enabled: true,\n phase: 'main',\n requires: ['popperOffsets'],\n fn: offset\n};","import computeOffsets from \"../utils/computeOffsets.js\";\n\nfunction popperOffsets(_ref) {\n var state = _ref.state,\n name = _ref.name;\n // Offsets are the actual position the popper needs to have to be\n // properly positioned near its reference element\n // This is the most basic placement, and will be adjusted by\n // the modifiers in the next step\n state.modifiersData[name] = computeOffsets({\n reference: state.rects.reference,\n element: state.rects.popper,\n strategy: 'absolute',\n placement: state.placement\n });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'popperOffsets',\n enabled: true,\n phase: 'read',\n fn: popperOffsets,\n data: {}\n};","import { top, left, right, bottom, start } from \"../enums.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getMainAxisFromPlacement from \"../utils/getMainAxisFromPlacement.js\";\nimport getAltAxis from \"../utils/getAltAxis.js\";\nimport { within, withinMaxClamp } from \"../utils/within.js\";\nimport getLayoutRect from \"../dom-utils/getLayoutRect.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\nimport getVariation from \"../utils/getVariation.js\";\nimport getFreshSideObject from \"../utils/getFreshSideObject.js\";\nimport { min as mathMin, max as mathMax } from \"../utils/math.js\";\n\nfunction preventOverflow(_ref) {\n var state = _ref.state,\n options = _ref.options,\n name = _ref.name;\n var _options$mainAxis = options.mainAxis,\n checkMainAxis = _options$mainAxis === void 0 ? true : _options$mainAxis,\n _options$altAxis = options.altAxis,\n checkAltAxis = _options$altAxis === void 0 ? false : _options$altAxis,\n boundary = options.boundary,\n rootBoundary = options.rootBoundary,\n altBoundary = options.altBoundary,\n padding = options.padding,\n _options$tether = options.tether,\n tether = _options$tether === void 0 ? true : _options$tether,\n _options$tetherOffset = options.tetherOffset,\n tetherOffset = _options$tetherOffset === void 0 ? 0 : _options$tetherOffset;\n var overflow = detectOverflow(state, {\n boundary: boundary,\n rootBoundary: rootBoundary,\n padding: padding,\n altBoundary: altBoundary\n });\n var basePlacement = getBasePlacement(state.placement);\n var variation = getVariation(state.placement);\n var isBasePlacement = !variation;\n var mainAxis = getMainAxisFromPlacement(basePlacement);\n var altAxis = getAltAxis(mainAxis);\n var popperOffsets = state.modifiersData.popperOffsets;\n var referenceRect = state.rects.reference;\n var popperRect = state.rects.popper;\n var tetherOffsetValue = typeof tetherOffset === 'function' ? tetherOffset(Object.assign({}, state.rects, {\n placement: state.placement\n })) : tetherOffset;\n var normalizedTetherOffsetValue = typeof tetherOffsetValue === 'number' ? {\n mainAxis: tetherOffsetValue,\n altAxis: tetherOffsetValue\n } : Object.assign({\n mainAxis: 0,\n altAxis: 0\n }, tetherOffsetValue);\n var offsetModifierState = state.modifiersData.offset ? state.modifiersData.offset[state.placement] : null;\n var data = {\n x: 0,\n y: 0\n };\n\n if (!popperOffsets) {\n return;\n }\n\n if (checkMainAxis) {\n var _offsetModifierState$;\n\n var mainSide = mainAxis === 'y' ? top : left;\n var altSide = mainAxis === 'y' ? bottom : right;\n var len = mainAxis === 'y' ? 'height' : 'width';\n var offset = popperOffsets[mainAxis];\n var min = offset + overflow[mainSide];\n var max = offset - overflow[altSide];\n var additive = tether ? -popperRect[len] / 2 : 0;\n var minLen = variation === start ? referenceRect[len] : popperRect[len];\n var maxLen = variation === start ? -popperRect[len] : -referenceRect[len]; // We need to include the arrow in the calculation so the arrow doesn't go\n // outside the reference bounds\n\n var arrowElement = state.elements.arrow;\n var arrowRect = tether && arrowElement ? getLayoutRect(arrowElement) : {\n width: 0,\n height: 0\n };\n var arrowPaddingObject = state.modifiersData['arrow#persistent'] ? state.modifiersData['arrow#persistent'].padding : getFreshSideObject();\n var arrowPaddingMin = arrowPaddingObject[mainSide];\n var arrowPaddingMax = arrowPaddingObject[altSide]; // If the reference length is smaller than the arrow length, we don't want\n // to include its full size in the calculation. If the reference is small\n // and near the edge of a boundary, the popper can overflow even if the\n // reference is not overflowing as well (e.g. virtual elements with no\n // width or height)\n\n var arrowLen = within(0, referenceRect[len], arrowRect[len]);\n var minOffset = isBasePlacement ? referenceRect[len] / 2 - additive - arrowLen - arrowPaddingMin - normalizedTetherOffsetValue.mainAxis : minLen - arrowLen - arrowPaddingMin - normalizedTetherOffsetValue.mainAxis;\n var maxOffset = isBasePlacement ? -referenceRect[len] / 2 + additive + arrowLen + arrowPaddingMax + normalizedTetherOffsetValue.mainAxis : maxLen + arrowLen + arrowPaddingMax + normalizedTetherOffsetValue.mainAxis;\n var arrowOffsetParent = state.elements.arrow && getOffsetParent(state.elements.arrow);\n var clientOffset = arrowOffsetParent ? mainAxis === 'y' ? arrowOffsetParent.clientTop || 0 : arrowOffsetParent.clientLeft || 0 : 0;\n var offsetModifierValue = (_offsetModifierState$ = offsetModifierState == null ? void 0 : offsetModifierState[mainAxis]) != null ? _offsetModifierState$ : 0;\n var tetherMin = offset + minOffset - offsetModifierValue - clientOffset;\n var tetherMax = offset + maxOffset - offsetModifierValue;\n var preventedOffset = within(tether ? mathMin(min, tetherMin) : min, offset, tether ? mathMax(max, tetherMax) : max);\n popperOffsets[mainAxis] = preventedOffset;\n data[mainAxis] = preventedOffset - offset;\n }\n\n if (checkAltAxis) {\n var _offsetModifierState$2;\n\n var _mainSide = mainAxis === 'x' ? top : left;\n\n var _altSide = mainAxis === 'x' ? bottom : right;\n\n var _offset = popperOffsets[altAxis];\n\n var _len = altAxis === 'y' ? 'height' : 'width';\n\n var _min = _offset + overflow[_mainSide];\n\n var _max = _offset - overflow[_altSide];\n\n var isOriginSide = [top, left].indexOf(basePlacement) !== -1;\n\n var _offsetModifierValue = (_offsetModifierState$2 = offsetModifierState == null ? void 0 : offsetModifierState[altAxis]) != null ? _offsetModifierState$2 : 0;\n\n var _tetherMin = isOriginSide ? _min : _offset - referenceRect[_len] - popperRect[_len] - _offsetModifierValue + normalizedTetherOffsetValue.altAxis;\n\n var _tetherMax = isOriginSide ? _offset + referenceRect[_len] + popperRect[_len] - _offsetModifierValue - normalizedTetherOffsetValue.altAxis : _max;\n\n var _preventedOffset = tether && isOriginSide ? withinMaxClamp(_tetherMin, _offset, _tetherMax) : within(tether ? _tetherMin : _min, _offset, tether ? _tetherMax : _max);\n\n popperOffsets[altAxis] = _preventedOffset;\n data[altAxis] = _preventedOffset - _offset;\n }\n\n state.modifiersData[name] = data;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'preventOverflow',\n enabled: true,\n phase: 'main',\n fn: preventOverflow,\n requiresIfExists: ['offset']\n};","export default function getAltAxis(axis) {\n return axis === 'x' ? 'y' : 'x';\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getNodeScroll from \"./getNodeScroll.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport isScrollParent from \"./isScrollParent.js\";\nimport { round } from \"../utils/math.js\";\n\nfunction isElementScaled(element) {\n var rect = element.getBoundingClientRect();\n var scaleX = round(rect.width) / element.offsetWidth || 1;\n var scaleY = round(rect.height) / element.offsetHeight || 1;\n return scaleX !== 1 || scaleY !== 1;\n} // Returns the composite rect of an element relative to its offsetParent.\n// Composite means it takes into account transforms as well as layout.\n\n\nexport default function getCompositeRect(elementOrVirtualElement, offsetParent, isFixed) {\n if (isFixed === void 0) {\n isFixed = false;\n }\n\n var isOffsetParentAnElement = isHTMLElement(offsetParent);\n var offsetParentIsScaled = isHTMLElement(offsetParent) && isElementScaled(offsetParent);\n var documentElement = getDocumentElement(offsetParent);\n var rect = getBoundingClientRect(elementOrVirtualElement, offsetParentIsScaled, isFixed);\n var scroll = {\n scrollLeft: 0,\n scrollTop: 0\n };\n var offsets = {\n x: 0,\n y: 0\n };\n\n if (isOffsetParentAnElement || !isOffsetParentAnElement && !isFixed) {\n if (getNodeName(offsetParent) !== 'body' || // https://github.com/popperjs/popper-core/issues/1078\n isScrollParent(documentElement)) {\n scroll = getNodeScroll(offsetParent);\n }\n\n if (isHTMLElement(offsetParent)) {\n offsets = getBoundingClientRect(offsetParent, true);\n offsets.x += offsetParent.clientLeft;\n offsets.y += offsetParent.clientTop;\n } else if (documentElement) {\n offsets.x = getWindowScrollBarX(documentElement);\n }\n }\n\n return {\n x: rect.left + scroll.scrollLeft - offsets.x,\n y: rect.top + scroll.scrollTop - offsets.y,\n width: rect.width,\n height: rect.height\n };\n}","import getWindowScroll from \"./getWindowScroll.js\";\nimport getWindow from \"./getWindow.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nimport getHTMLElementScroll from \"./getHTMLElementScroll.js\";\nexport default function getNodeScroll(node) {\n if (node === getWindow(node) || !isHTMLElement(node)) {\n return getWindowScroll(node);\n } else {\n return getHTMLElementScroll(node);\n }\n}","export default function getHTMLElementScroll(element) {\n return {\n scrollLeft: element.scrollLeft,\n scrollTop: element.scrollTop\n };\n}","import { modifierPhases } from \"../enums.js\"; // source: https://stackoverflow.com/questions/49875255\n\nfunction order(modifiers) {\n var map = new Map();\n var visited = new Set();\n var result = [];\n modifiers.forEach(function (modifier) {\n map.set(modifier.name, modifier);\n }); // On visiting object, check for its dependencies and visit them recursively\n\n function sort(modifier) {\n visited.add(modifier.name);\n var requires = [].concat(modifier.requires || [], modifier.requiresIfExists || []);\n requires.forEach(function (dep) {\n if (!visited.has(dep)) {\n var depModifier = map.get(dep);\n\n if (depModifier) {\n sort(depModifier);\n }\n }\n });\n result.push(modifier);\n }\n\n modifiers.forEach(function (modifier) {\n if (!visited.has(modifier.name)) {\n // check for visited object\n sort(modifier);\n }\n });\n return result;\n}\n\nexport default function orderModifiers(modifiers) {\n // order based on dependencies\n var orderedModifiers = order(modifiers); // order based on phase\n\n return modifierPhases.reduce(function (acc, phase) {\n return acc.concat(orderedModifiers.filter(function (modifier) {\n return modifier.phase === phase;\n }));\n }, []);\n}","import getCompositeRect from \"./dom-utils/getCompositeRect.js\";\nimport getLayoutRect from \"./dom-utils/getLayoutRect.js\";\nimport listScrollParents from \"./dom-utils/listScrollParents.js\";\nimport getOffsetParent from \"./dom-utils/getOffsetParent.js\";\nimport orderModifiers from \"./utils/orderModifiers.js\";\nimport debounce from \"./utils/debounce.js\";\nimport mergeByName from \"./utils/mergeByName.js\";\nimport detectOverflow from \"./utils/detectOverflow.js\";\nimport { isElement } from \"./dom-utils/instanceOf.js\";\nvar DEFAULT_OPTIONS = {\n placement: 'bottom',\n modifiers: [],\n strategy: 'absolute'\n};\n\nfunction areValidElements() {\n for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {\n args[_key] = arguments[_key];\n }\n\n return !args.some(function (element) {\n return !(element && typeof element.getBoundingClientRect === 'function');\n });\n}\n\nexport function popperGenerator(generatorOptions) {\n if (generatorOptions === void 0) {\n generatorOptions = {};\n }\n\n var _generatorOptions = generatorOptions,\n _generatorOptions$def = _generatorOptions.defaultModifiers,\n defaultModifiers = _generatorOptions$def === void 0 ? [] : _generatorOptions$def,\n _generatorOptions$def2 = _generatorOptions.defaultOptions,\n defaultOptions = _generatorOptions$def2 === void 0 ? DEFAULT_OPTIONS : _generatorOptions$def2;\n return function createPopper(reference, popper, options) {\n if (options === void 0) {\n options = defaultOptions;\n }\n\n var state = {\n placement: 'bottom',\n orderedModifiers: [],\n options: Object.assign({}, DEFAULT_OPTIONS, defaultOptions),\n modifiersData: {},\n elements: {\n reference: reference,\n popper: popper\n },\n attributes: {},\n styles: {}\n };\n var effectCleanupFns = [];\n var isDestroyed = false;\n var instance = {\n state: state,\n setOptions: function setOptions(setOptionsAction) {\n var options = typeof setOptionsAction === 'function' ? setOptionsAction(state.options) : setOptionsAction;\n cleanupModifierEffects();\n state.options = Object.assign({}, defaultOptions, state.options, options);\n state.scrollParents = {\n reference: isElement(reference) ? listScrollParents(reference) : reference.contextElement ? listScrollParents(reference.contextElement) : [],\n popper: listScrollParents(popper)\n }; // Orders the modifiers based on their dependencies and `phase`\n // properties\n\n var orderedModifiers = orderModifiers(mergeByName([].concat(defaultModifiers, state.options.modifiers))); // Strip out disabled modifiers\n\n state.orderedModifiers = orderedModifiers.filter(function (m) {\n return m.enabled;\n });\n runModifierEffects();\n return instance.update();\n },\n // Sync update – it will always be executed, even if not necessary. This\n // is useful for low frequency updates where sync behavior simplifies the\n // logic.\n // For high frequency updates (e.g. `resize` and `scroll` events), always\n // prefer the async Popper#update method\n forceUpdate: function forceUpdate() {\n if (isDestroyed) {\n return;\n }\n\n var _state$elements = state.elements,\n reference = _state$elements.reference,\n popper = _state$elements.popper; // Don't proceed if `reference` or `popper` are not valid elements\n // anymore\n\n if (!areValidElements(reference, popper)) {\n return;\n } // Store the reference and popper rects to be read by modifiers\n\n\n state.rects = {\n reference: getCompositeRect(reference, getOffsetParent(popper), state.options.strategy === 'fixed'),\n popper: getLayoutRect(popper)\n }; // Modifiers have the ability to reset the current update cycle. The\n // most common use case for this is the `flip` modifier changing the\n // placement, which then needs to re-run all the modifiers, because the\n // logic was previously ran for the previous placement and is therefore\n // stale/incorrect\n\n state.reset = false;\n state.placement = state.options.placement; // On each update cycle, the `modifiersData` property for each modifier\n // is filled with the initial data specified by the modifier. This means\n // it doesn't persist and is fresh on each update.\n // To ensure persistent data, use `${name}#persistent`\n\n state.orderedModifiers.forEach(function (modifier) {\n return state.modifiersData[modifier.name] = Object.assign({}, modifier.data);\n });\n\n for (var index = 0; index < state.orderedModifiers.length; index++) {\n if (state.reset === true) {\n state.reset = false;\n index = -1;\n continue;\n }\n\n var _state$orderedModifie = state.orderedModifiers[index],\n fn = _state$orderedModifie.fn,\n _state$orderedModifie2 = _state$orderedModifie.options,\n _options = _state$orderedModifie2 === void 0 ? {} : _state$orderedModifie2,\n name = _state$orderedModifie.name;\n\n if (typeof fn === 'function') {\n state = fn({\n state: state,\n options: _options,\n name: name,\n instance: instance\n }) || state;\n }\n }\n },\n // Async and optimistically optimized update – it will not be executed if\n // not necessary (debounced to run at most once-per-tick)\n update: debounce(function () {\n return new Promise(function (resolve) {\n instance.forceUpdate();\n resolve(state);\n });\n }),\n destroy: function destroy() {\n cleanupModifierEffects();\n isDestroyed = true;\n }\n };\n\n if (!areValidElements(reference, popper)) {\n return instance;\n }\n\n instance.setOptions(options).then(function (state) {\n if (!isDestroyed && options.onFirstUpdate) {\n options.onFirstUpdate(state);\n }\n }); // Modifiers have the ability to execute arbitrary code before the first\n // update cycle runs. They will be executed in the same order as the update\n // cycle. This is useful when a modifier adds some persistent data that\n // other modifiers need to use, but the modifier is run after the dependent\n // one.\n\n function runModifierEffects() {\n state.orderedModifiers.forEach(function (_ref) {\n var name = _ref.name,\n _ref$options = _ref.options,\n options = _ref$options === void 0 ? {} : _ref$options,\n effect = _ref.effect;\n\n if (typeof effect === 'function') {\n var cleanupFn = effect({\n state: state,\n name: name,\n instance: instance,\n options: options\n });\n\n var noopFn = function noopFn() {};\n\n effectCleanupFns.push(cleanupFn || noopFn);\n }\n });\n }\n\n function cleanupModifierEffects() {\n effectCleanupFns.forEach(function (fn) {\n return fn();\n });\n effectCleanupFns = [];\n }\n\n return instance;\n };\n}\nexport var createPopper = /*#__PURE__*/popperGenerator(); // eslint-disable-next-line import/no-unused-modules\n\nexport { detectOverflow };","export default function debounce(fn) {\n var pending;\n return function () {\n if (!pending) {\n pending = new Promise(function (resolve) {\n Promise.resolve().then(function () {\n pending = undefined;\n resolve(fn());\n });\n });\n }\n\n return pending;\n };\n}","export default function mergeByName(modifiers) {\n var merged = modifiers.reduce(function (merged, current) {\n var existing = merged[current.name];\n merged[current.name] = existing ? Object.assign({}, existing, current, {\n options: Object.assign({}, existing.options, current.options),\n data: Object.assign({}, existing.data, current.data)\n }) : current;\n return merged;\n }, {}); // IE11 does not support Object.values\n\n return Object.keys(merged).map(function (key) {\n return merged[key];\n });\n}","import { popperGenerator, detectOverflow } from \"./createPopper.js\";\nimport eventListeners from \"./modifiers/eventListeners.js\";\nimport popperOffsets from \"./modifiers/popperOffsets.js\";\nimport computeStyles from \"./modifiers/computeStyles.js\";\nimport applyStyles from \"./modifiers/applyStyles.js\";\nvar defaultModifiers = [eventListeners, popperOffsets, computeStyles, applyStyles];\nvar createPopper = /*#__PURE__*/popperGenerator({\n defaultModifiers: defaultModifiers\n}); // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper, popperGenerator, defaultModifiers, detectOverflow };","import { popperGenerator, detectOverflow } from \"./createPopper.js\";\nimport eventListeners from \"./modifiers/eventListeners.js\";\nimport popperOffsets from \"./modifiers/popperOffsets.js\";\nimport computeStyles from \"./modifiers/computeStyles.js\";\nimport applyStyles from \"./modifiers/applyStyles.js\";\nimport offset from \"./modifiers/offset.js\";\nimport flip from \"./modifiers/flip.js\";\nimport preventOverflow from \"./modifiers/preventOverflow.js\";\nimport arrow from \"./modifiers/arrow.js\";\nimport hide from \"./modifiers/hide.js\";\nvar defaultModifiers = [eventListeners, popperOffsets, computeStyles, applyStyles, offset, flip, preventOverflow, arrow, hide];\nvar createPopper = /*#__PURE__*/popperGenerator({\n defaultModifiers: defaultModifiers\n}); // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper, popperGenerator, defaultModifiers, detectOverflow }; // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper as createPopperLite } from \"./popper-lite.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport * from \"./modifiers/index.js\";","/**\n * --------------------------------------------------------------------------\n * Bootstrap dropdown.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport * as Popper from '@popperjs/core'\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport Manipulator from './dom/manipulator.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport {\n defineJQueryPlugin,\n execute,\n getElement,\n getNextActiveElement,\n isDisabled,\n isElement,\n isRTL,\n isVisible,\n noop\n} from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'dropdown'\nconst DATA_KEY = 'bs.dropdown'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst ESCAPE_KEY = 'Escape'\nconst TAB_KEY = 'Tab'\nconst ARROW_UP_KEY = 'ArrowUp'\nconst ARROW_DOWN_KEY = 'ArrowDown'\nconst RIGHT_MOUSE_BUTTON = 2 // MouseEvent.button value for the secondary button, usually the right button\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYDOWN_DATA_API = `keydown${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYUP_DATA_API = `keyup${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_DROPUP = 'dropup'\nconst CLASS_NAME_DROPEND = 'dropend'\nconst CLASS_NAME_DROPSTART = 'dropstart'\nconst CLASS_NAME_DROPUP_CENTER = 'dropup-center'\nconst CLASS_NAME_DROPDOWN_CENTER = 'dropdown-center'\n\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"dropdown\"]:not(.disabled):not(:disabled)'\nconst SELECTOR_DATA_TOGGLE_SHOWN = `${SELECTOR_DATA_TOGGLE}.${CLASS_NAME_SHOW}`\nconst SELECTOR_MENU = '.dropdown-menu'\nconst SELECTOR_NAVBAR = '.navbar'\nconst SELECTOR_NAVBAR_NAV = '.navbar-nav'\nconst SELECTOR_VISIBLE_ITEMS = '.dropdown-menu .dropdown-item:not(.disabled):not(:disabled)'\n\nconst PLACEMENT_TOP = isRTL() ? 'top-end' : 'top-start'\nconst PLACEMENT_TOPEND = isRTL() ? 'top-start' : 'top-end'\nconst PLACEMENT_BOTTOM = isRTL() ? 'bottom-end' : 'bottom-start'\nconst PLACEMENT_BOTTOMEND = isRTL() ? 'bottom-start' : 'bottom-end'\nconst PLACEMENT_RIGHT = isRTL() ? 'left-start' : 'right-start'\nconst PLACEMENT_LEFT = isRTL() ? 'right-start' : 'left-start'\nconst PLACEMENT_TOPCENTER = 'top'\nconst PLACEMENT_BOTTOMCENTER = 'bottom'\n\nconst Default = {\n autoClose: true,\n boundary: 'clippingParents',\n display: 'dynamic',\n offset: [0, 2],\n popperConfig: null,\n reference: 'toggle'\n}\n\nconst DefaultType = {\n autoClose: '(boolean|string)',\n boundary: '(string|element)',\n display: 'string',\n offset: '(array|string|function)',\n popperConfig: '(null|object|function)',\n reference: '(string|element|object)'\n}\n\n/**\n * Class definition\n */\n\nclass Dropdown extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._popper = null\n this._parent = this._element.parentNode // dropdown wrapper\n // TODO: v6 revert #37011 & change markup https://getbootstrap.com/docs/5.3/forms/input-group/\n this._menu = SelectorEngine.next(this._element, SELECTOR_MENU)[0] ||\n SelectorEngine.prev(this._element, SELECTOR_MENU)[0] ||\n SelectorEngine.findOne(SELECTOR_MENU, this._parent)\n this._inNavbar = this._detectNavbar()\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n toggle() {\n return this._isShown() ? this.hide() : this.show()\n }\n\n show() {\n if (isDisabled(this._element) || this._isShown()) {\n return\n }\n\n const relatedTarget = {\n relatedTarget: this._element\n }\n\n const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, relatedTarget)\n\n if (showEvent.defaultPrevented) {\n return\n }\n\n this._createPopper()\n\n // If this is a touch-enabled device we add extra\n // empty mouseover listeners to the body's immediate children;\n // only needed because of broken event delegation on iOS\n // https://www.quirksmode.org/blog/archives/2014/02/mouse_event_bub.html\n if ('ontouchstart' in document.documentElement && !this._parent.closest(SELECTOR_NAVBAR_NAV)) {\n for (const element of [].concat(...document.body.children)) {\n EventHandler.on(element, 'mouseover', noop)\n }\n }\n\n this._element.focus()\n this._element.setAttribute('aria-expanded', true)\n\n this._menu.classList.add(CLASS_NAME_SHOW)\n this._element.classList.add(CLASS_NAME_SHOW)\n EventHandler.trigger(this._element, EVENT_SHOWN, relatedTarget)\n }\n\n hide() {\n if (isDisabled(this._element) || !this._isShown()) {\n return\n }\n\n const relatedTarget = {\n relatedTarget: this._element\n }\n\n this._completeHide(relatedTarget)\n }\n\n dispose() {\n if (this._popper) {\n this._popper.destroy()\n }\n\n super.dispose()\n }\n\n update() {\n this._inNavbar = this._detectNavbar()\n if (this._popper) {\n this._popper.update()\n }\n }\n\n // Private\n _completeHide(relatedTarget) {\n const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE, relatedTarget)\n if (hideEvent.defaultPrevented) {\n return\n }\n\n // If this is a touch-enabled device we remove the extra\n // empty mouseover listeners we added for iOS support\n if ('ontouchstart' in document.documentElement) {\n for (const element of [].concat(...document.body.children)) {\n EventHandler.off(element, 'mouseover', noop)\n }\n }\n\n if (this._popper) {\n this._popper.destroy()\n }\n\n this._menu.classList.remove(CLASS_NAME_SHOW)\n this._element.classList.remove(CLASS_NAME_SHOW)\n this._element.setAttribute('aria-expanded', 'false')\n Manipulator.removeDataAttribute(this._menu, 'popper')\n EventHandler.trigger(this._element, EVENT_HIDDEN, relatedTarget)\n }\n\n _getConfig(config) {\n config = super._getConfig(config)\n\n if (typeof config.reference === 'object' && !isElement(config.reference) &&\n typeof config.reference.getBoundingClientRect !== 'function'\n ) {\n // Popper virtual elements require a getBoundingClientRect method\n throw new TypeError(`${NAME.toUpperCase()}: Option \"reference\" provided type \"object\" without a required \"getBoundingClientRect\" method.`)\n }\n\n return config\n }\n\n _createPopper() {\n if (typeof Popper === 'undefined') {\n throw new TypeError('Bootstrap\\'s dropdowns require Popper (https://popper.js.org)')\n }\n\n let referenceElement = this._element\n\n if (this._config.reference === 'parent') {\n referenceElement = this._parent\n } else if (isElement(this._config.reference)) {\n referenceElement = getElement(this._config.reference)\n } else if (typeof this._config.reference === 'object') {\n referenceElement = this._config.reference\n }\n\n const popperConfig = this._getPopperConfig()\n this._popper = Popper.createPopper(referenceElement, this._menu, popperConfig)\n }\n\n _isShown() {\n return this._menu.classList.contains(CLASS_NAME_SHOW)\n }\n\n _getPlacement() {\n const parentDropdown = this._parent\n\n if (parentDropdown.classList.contains(CLASS_NAME_DROPEND)) {\n return PLACEMENT_RIGHT\n }\n\n if (parentDropdown.classList.contains(CLASS_NAME_DROPSTART)) {\n return PLACEMENT_LEFT\n }\n\n if (parentDropdown.classList.contains(CLASS_NAME_DROPUP_CENTER)) {\n return PLACEMENT_TOPCENTER\n }\n\n if (parentDropdown.classList.contains(CLASS_NAME_DROPDOWN_CENTER)) {\n return PLACEMENT_BOTTOMCENTER\n }\n\n // We need to trim the value because custom properties can also include spaces\n const isEnd = getComputedStyle(this._menu).getPropertyValue('--bs-position').trim() === 'end'\n\n if (parentDropdown.classList.contains(CLASS_NAME_DROPUP)) {\n return isEnd ? PLACEMENT_TOPEND : PLACEMENT_TOP\n }\n\n return isEnd ? PLACEMENT_BOTTOMEND : PLACEMENT_BOTTOM\n }\n\n _detectNavbar() {\n return this._element.closest(SELECTOR_NAVBAR) !== null\n }\n\n _getOffset() {\n const { offset } = this._config\n\n if (typeof offset === 'string') {\n return offset.split(',').map(value => Number.parseInt(value, 10))\n }\n\n if (typeof offset === 'function') {\n return popperData => offset(popperData, this._element)\n }\n\n return offset\n }\n\n _getPopperConfig() {\n const defaultBsPopperConfig = {\n placement: this._getPlacement(),\n modifiers: [{\n name: 'preventOverflow',\n options: {\n boundary: this._config.boundary\n }\n },\n {\n name: 'offset',\n options: {\n offset: this._getOffset()\n }\n }]\n }\n\n // Disable Popper if we have a static display or Dropdown is in Navbar\n if (this._inNavbar || this._config.display === 'static') {\n Manipulator.setDataAttribute(this._menu, 'popper', 'static') // TODO: v6 remove\n defaultBsPopperConfig.modifiers = [{\n name: 'applyStyles',\n enabled: false\n }]\n }\n\n return {\n ...defaultBsPopperConfig,\n ...execute(this._config.popperConfig, [defaultBsPopperConfig])\n }\n }\n\n _selectMenuItem({ key, target }) {\n const items = SelectorEngine.find(SELECTOR_VISIBLE_ITEMS, this._menu).filter(element => isVisible(element))\n\n if (!items.length) {\n return\n }\n\n // if target isn't included in items (e.g. when expanding the dropdown)\n // allow cycling to get the last item in case key equals ARROW_UP_KEY\n getNextActiveElement(items, target, key === ARROW_DOWN_KEY, !items.includes(target)).focus()\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Dropdown.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n })\n }\n\n static clearMenus(event) {\n if (event.button === RIGHT_MOUSE_BUTTON || (event.type === 'keyup' && event.key !== TAB_KEY)) {\n return\n }\n\n const openToggles = SelectorEngine.find(SELECTOR_DATA_TOGGLE_SHOWN)\n\n for (const toggle of openToggles) {\n const context = Dropdown.getInstance(toggle)\n if (!context || context._config.autoClose === false) {\n continue\n }\n\n const composedPath = event.composedPath()\n const isMenuTarget = composedPath.includes(context._menu)\n if (\n composedPath.includes(context._element) ||\n (context._config.autoClose === 'inside' && !isMenuTarget) ||\n (context._config.autoClose === 'outside' && isMenuTarget)\n ) {\n continue\n }\n\n // Tab navigation through the dropdown menu or events from contained inputs shouldn't close the menu\n if (context._menu.contains(event.target) && ((event.type === 'keyup' && event.key === TAB_KEY) || /input|select|option|textarea|form/i.test(event.target.tagName))) {\n continue\n }\n\n const relatedTarget = { relatedTarget: context._element }\n\n if (event.type === 'click') {\n relatedTarget.clickEvent = event\n }\n\n context._completeHide(relatedTarget)\n }\n }\n\n static dataApiKeydownHandler(event) {\n // If not an UP | DOWN | ESCAPE key => not a dropdown command\n // If input/textarea && if key is other than ESCAPE => not a dropdown command\n\n const isInput = /input|textarea/i.test(event.target.tagName)\n const isEscapeEvent = event.key === ESCAPE_KEY\n const isUpOrDownEvent = [ARROW_UP_KEY, ARROW_DOWN_KEY].includes(event.key)\n\n if (!isUpOrDownEvent && !isEscapeEvent) {\n return\n }\n\n if (isInput && !isEscapeEvent) {\n return\n }\n\n event.preventDefault()\n\n // TODO: v6 revert #37011 & change markup https://getbootstrap.com/docs/5.3/forms/input-group/\n const getToggleButton = this.matches(SELECTOR_DATA_TOGGLE) ?\n this :\n (SelectorEngine.prev(this, SELECTOR_DATA_TOGGLE)[0] ||\n SelectorEngine.next(this, SELECTOR_DATA_TOGGLE)[0] ||\n SelectorEngine.findOne(SELECTOR_DATA_TOGGLE, event.delegateTarget.parentNode))\n\n const instance = Dropdown.getOrCreateInstance(getToggleButton)\n\n if (isUpOrDownEvent) {\n event.stopPropagation()\n instance.show()\n instance._selectMenuItem(event)\n return\n }\n\n if (instance._isShown()) { // else is escape and we check if it is shown\n event.stopPropagation()\n instance.hide()\n getToggleButton.focus()\n }\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_KEYDOWN_DATA_API, SELECTOR_DATA_TOGGLE, Dropdown.dataApiKeydownHandler)\nEventHandler.on(document, EVENT_KEYDOWN_DATA_API, SELECTOR_MENU, Dropdown.dataApiKeydownHandler)\nEventHandler.on(document, EVENT_CLICK_DATA_API, Dropdown.clearMenus)\nEventHandler.on(document, EVENT_KEYUP_DATA_API, Dropdown.clearMenus)\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n event.preventDefault()\n Dropdown.getOrCreateInstance(this).toggle()\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Dropdown)\n\nexport default Dropdown\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/backdrop.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport Config from './config.js'\nimport { execute, executeAfterTransition, getElement, reflow } from './index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'backdrop'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst EVENT_MOUSEDOWN = `mousedown.bs.${NAME}`\n\nconst Default = {\n className: 'modal-backdrop',\n clickCallback: null,\n isAnimated: false,\n isVisible: true, // if false, we use the backdrop helper without adding any element to the dom\n rootElement: 'body' // give the choice to place backdrop under different elements\n}\n\nconst DefaultType = {\n className: 'string',\n clickCallback: '(function|null)',\n isAnimated: 'boolean',\n isVisible: 'boolean',\n rootElement: '(element|string)'\n}\n\n/**\n * Class definition\n */\n\nclass Backdrop extends Config {\n constructor(config) {\n super()\n this._config = this._getConfig(config)\n this._isAppended = false\n this._element = null\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n show(callback) {\n if (!this._config.isVisible) {\n execute(callback)\n return\n }\n\n this._append()\n\n const element = this._getElement()\n if (this._config.isAnimated) {\n reflow(element)\n }\n\n element.classList.add(CLASS_NAME_SHOW)\n\n this._emulateAnimation(() => {\n execute(callback)\n })\n }\n\n hide(callback) {\n if (!this._config.isVisible) {\n execute(callback)\n return\n }\n\n this._getElement().classList.remove(CLASS_NAME_SHOW)\n\n this._emulateAnimation(() => {\n this.dispose()\n execute(callback)\n })\n }\n\n dispose() {\n if (!this._isAppended) {\n return\n }\n\n EventHandler.off(this._element, EVENT_MOUSEDOWN)\n\n this._element.remove()\n this._isAppended = false\n }\n\n // Private\n _getElement() {\n if (!this._element) {\n const backdrop = document.createElement('div')\n backdrop.className = this._config.className\n if (this._config.isAnimated) {\n backdrop.classList.add(CLASS_NAME_FADE)\n }\n\n this._element = backdrop\n }\n\n return this._element\n }\n\n _configAfterMerge(config) {\n // use getElement() with the default \"body\" to get a fresh Element on each instantiation\n config.rootElement = getElement(config.rootElement)\n return config\n }\n\n _append() {\n if (this._isAppended) {\n return\n }\n\n const element = this._getElement()\n this._config.rootElement.append(element)\n\n EventHandler.on(element, EVENT_MOUSEDOWN, () => {\n execute(this._config.clickCallback)\n })\n\n this._isAppended = true\n }\n\n _emulateAnimation(callback) {\n executeAfterTransition(callback, this._getElement(), this._config.isAnimated)\n }\n}\n\nexport default Backdrop\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/focustrap.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport SelectorEngine from '../dom/selector-engine.js'\nimport Config from './config.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'focustrap'\nconst DATA_KEY = 'bs.focustrap'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst EVENT_FOCUSIN = `focusin${EVENT_KEY}`\nconst EVENT_KEYDOWN_TAB = `keydown.tab${EVENT_KEY}`\n\nconst TAB_KEY = 'Tab'\nconst TAB_NAV_FORWARD = 'forward'\nconst TAB_NAV_BACKWARD = 'backward'\n\nconst Default = {\n autofocus: true,\n trapElement: null // The element to trap focus inside of\n}\n\nconst DefaultType = {\n autofocus: 'boolean',\n trapElement: 'element'\n}\n\n/**\n * Class definition\n */\n\nclass FocusTrap extends Config {\n constructor(config) {\n super()\n this._config = this._getConfig(config)\n this._isActive = false\n this._lastTabNavDirection = null\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n activate() {\n if (this._isActive) {\n return\n }\n\n if (this._config.autofocus) {\n this._config.trapElement.focus()\n }\n\n EventHandler.off(document, EVENT_KEY) // guard against infinite focus loop\n EventHandler.on(document, EVENT_FOCUSIN, event => this._handleFocusin(event))\n EventHandler.on(document, EVENT_KEYDOWN_TAB, event => this._handleKeydown(event))\n\n this._isActive = true\n }\n\n deactivate() {\n if (!this._isActive) {\n return\n }\n\n this._isActive = false\n EventHandler.off(document, EVENT_KEY)\n }\n\n // Private\n _handleFocusin(event) {\n const { trapElement } = this._config\n\n if (event.target === document || event.target === trapElement || trapElement.contains(event.target)) {\n return\n }\n\n const elements = SelectorEngine.focusableChildren(trapElement)\n\n if (elements.length === 0) {\n trapElement.focus()\n } else if (this._lastTabNavDirection === TAB_NAV_BACKWARD) {\n elements[elements.length - 1].focus()\n } else {\n elements[0].focus()\n }\n }\n\n _handleKeydown(event) {\n if (event.key !== TAB_KEY) {\n return\n }\n\n this._lastTabNavDirection = event.shiftKey ? TAB_NAV_BACKWARD : TAB_NAV_FORWARD\n }\n}\n\nexport default FocusTrap\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/scrollBar.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Manipulator from '../dom/manipulator.js'\nimport SelectorEngine from '../dom/selector-engine.js'\nimport { isElement } from './index.js'\n\n/**\n * Constants\n */\n\nconst SELECTOR_FIXED_CONTENT = '.fixed-top, .fixed-bottom, .is-fixed, .sticky-top'\nconst SELECTOR_STICKY_CONTENT = '.sticky-top'\nconst PROPERTY_PADDING = 'padding-right'\nconst PROPERTY_MARGIN = 'margin-right'\n\n/**\n * Class definition\n */\n\nclass ScrollBarHelper {\n constructor() {\n this._element = document.body\n }\n\n // Public\n getWidth() {\n // https://developer.mozilla.org/en-US/docs/Web/API/Window/innerWidth#usage_notes\n const documentWidth = document.documentElement.clientWidth\n return Math.abs(window.innerWidth - documentWidth)\n }\n\n hide() {\n const width = this.getWidth()\n this._disableOverFlow()\n // give padding to element to balance the hidden scrollbar width\n this._setElementAttributes(this._element, PROPERTY_PADDING, calculatedValue => calculatedValue + width)\n // trick: We adjust positive paddingRight and negative marginRight to sticky-top elements to keep showing fullwidth\n this._setElementAttributes(SELECTOR_FIXED_CONTENT, PROPERTY_PADDING, calculatedValue => calculatedValue + width)\n this._setElementAttributes(SELECTOR_STICKY_CONTENT, PROPERTY_MARGIN, calculatedValue => calculatedValue - width)\n }\n\n reset() {\n this._resetElementAttributes(this._element, 'overflow')\n this._resetElementAttributes(this._element, PROPERTY_PADDING)\n this._resetElementAttributes(SELECTOR_FIXED_CONTENT, PROPERTY_PADDING)\n this._resetElementAttributes(SELECTOR_STICKY_CONTENT, PROPERTY_MARGIN)\n }\n\n isOverflowing() {\n return this.getWidth() > 0\n }\n\n // Private\n _disableOverFlow() {\n this._saveInitialAttribute(this._element, 'overflow')\n this._element.style.overflow = 'hidden'\n }\n\n _setElementAttributes(selector, styleProperty, callback) {\n const scrollbarWidth = this.getWidth()\n const manipulationCallBack = element => {\n if (element !== this._element && window.innerWidth > element.clientWidth + scrollbarWidth) {\n return\n }\n\n this._saveInitialAttribute(element, styleProperty)\n const calculatedValue = window.getComputedStyle(element).getPropertyValue(styleProperty)\n element.style.setProperty(styleProperty, `${callback(Number.parseFloat(calculatedValue))}px`)\n }\n\n this._applyManipulationCallback(selector, manipulationCallBack)\n }\n\n _saveInitialAttribute(element, styleProperty) {\n const actualValue = element.style.getPropertyValue(styleProperty)\n if (actualValue) {\n Manipulator.setDataAttribute(element, styleProperty, actualValue)\n }\n }\n\n _resetElementAttributes(selector, styleProperty) {\n const manipulationCallBack = element => {\n const value = Manipulator.getDataAttribute(element, styleProperty)\n // We only want to remove the property if the value is `null`; the value can also be zero\n if (value === null) {\n element.style.removeProperty(styleProperty)\n return\n }\n\n Manipulator.removeDataAttribute(element, styleProperty)\n element.style.setProperty(styleProperty, value)\n }\n\n this._applyManipulationCallback(selector, manipulationCallBack)\n }\n\n _applyManipulationCallback(selector, callBack) {\n if (isElement(selector)) {\n callBack(selector)\n return\n }\n\n for (const sel of SelectorEngine.find(selector, this._element)) {\n callBack(sel)\n }\n }\n}\n\nexport default ScrollBarHelper\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap modal.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport Backdrop from './util/backdrop.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport FocusTrap from './util/focustrap.js'\nimport { defineJQueryPlugin, isRTL, isVisible, reflow } from './util/index.js'\nimport ScrollBarHelper from './util/scrollbar.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'modal'\nconst DATA_KEY = 'bs.modal'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\nconst ESCAPE_KEY = 'Escape'\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDE_PREVENTED = `hidePrevented${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_RESIZE = `resize${EVENT_KEY}`\nconst EVENT_CLICK_DISMISS = `click.dismiss${EVENT_KEY}`\nconst EVENT_MOUSEDOWN_DISMISS = `mousedown.dismiss${EVENT_KEY}`\nconst EVENT_KEYDOWN_DISMISS = `keydown.dismiss${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_OPEN = 'modal-open'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_STATIC = 'modal-static'\n\nconst OPEN_SELECTOR = '.modal.show'\nconst SELECTOR_DIALOG = '.modal-dialog'\nconst SELECTOR_MODAL_BODY = '.modal-body'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"modal\"]'\n\nconst Default = {\n backdrop: true,\n focus: true,\n keyboard: true\n}\n\nconst DefaultType = {\n backdrop: '(boolean|string)',\n focus: 'boolean',\n keyboard: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Modal extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._dialog = SelectorEngine.findOne(SELECTOR_DIALOG, this._element)\n this._backdrop = this._initializeBackDrop()\n this._focustrap = this._initializeFocusTrap()\n this._isShown = false\n this._isTransitioning = false\n this._scrollBar = new ScrollBarHelper()\n\n this._addEventListeners()\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n toggle(relatedTarget) {\n return this._isShown ? this.hide() : this.show(relatedTarget)\n }\n\n show(relatedTarget) {\n if (this._isShown || this._isTransitioning) {\n return\n }\n\n const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, {\n relatedTarget\n })\n\n if (showEvent.defaultPrevented) {\n return\n }\n\n this._isShown = true\n this._isTransitioning = true\n\n this._scrollBar.hide()\n\n document.body.classList.add(CLASS_NAME_OPEN)\n\n this._adjustDialog()\n\n this._backdrop.show(() => this._showElement(relatedTarget))\n }\n\n hide() {\n if (!this._isShown || this._isTransitioning) {\n return\n }\n\n const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n if (hideEvent.defaultPrevented) {\n return\n }\n\n this._isShown = false\n this._isTransitioning = true\n this._focustrap.deactivate()\n\n this._element.classList.remove(CLASS_NAME_SHOW)\n\n this._queueCallback(() => this._hideModal(), this._element, this._isAnimated())\n }\n\n dispose() {\n EventHandler.off(window, EVENT_KEY)\n EventHandler.off(this._dialog, EVENT_KEY)\n\n this._backdrop.dispose()\n this._focustrap.deactivate()\n\n super.dispose()\n }\n\n handleUpdate() {\n this._adjustDialog()\n }\n\n // Private\n _initializeBackDrop() {\n return new Backdrop({\n isVisible: Boolean(this._config.backdrop), // 'static' option will be translated to true, and booleans will keep their value,\n isAnimated: this._isAnimated()\n })\n }\n\n _initializeFocusTrap() {\n return new FocusTrap({\n trapElement: this._element\n })\n }\n\n _showElement(relatedTarget) {\n // try to append dynamic modal\n if (!document.body.contains(this._element)) {\n document.body.append(this._element)\n }\n\n this._element.style.display = 'block'\n this._element.removeAttribute('aria-hidden')\n this._element.setAttribute('aria-modal', true)\n this._element.setAttribute('role', 'dialog')\n this._element.scrollTop = 0\n\n const modalBody = SelectorEngine.findOne(SELECTOR_MODAL_BODY, this._dialog)\n if (modalBody) {\n modalBody.scrollTop = 0\n }\n\n reflow(this._element)\n\n this._element.classList.add(CLASS_NAME_SHOW)\n\n const transitionComplete = () => {\n if (this._config.focus) {\n this._focustrap.activate()\n }\n\n this._isTransitioning = false\n EventHandler.trigger(this._element, EVENT_SHOWN, {\n relatedTarget\n })\n }\n\n this._queueCallback(transitionComplete, this._dialog, this._isAnimated())\n }\n\n _addEventListeners() {\n EventHandler.on(this._element, EVENT_KEYDOWN_DISMISS, event => {\n if (event.key !== ESCAPE_KEY) {\n return\n }\n\n if (this._config.keyboard) {\n this.hide()\n return\n }\n\n this._triggerBackdropTransition()\n })\n\n EventHandler.on(window, EVENT_RESIZE, () => {\n if (this._isShown && !this._isTransitioning) {\n this._adjustDialog()\n }\n })\n\n EventHandler.on(this._element, EVENT_MOUSEDOWN_DISMISS, event => {\n // a bad trick to segregate clicks that may start inside dialog but end outside, and avoid listen to scrollbar clicks\n EventHandler.one(this._element, EVENT_CLICK_DISMISS, event2 => {\n if (this._element !== event.target || this._element !== event2.target) {\n return\n }\n\n if (this._config.backdrop === 'static') {\n this._triggerBackdropTransition()\n return\n }\n\n if (this._config.backdrop) {\n this.hide()\n }\n })\n })\n }\n\n _hideModal() {\n this._element.style.display = 'none'\n this._element.setAttribute('aria-hidden', true)\n this._element.removeAttribute('aria-modal')\n this._element.removeAttribute('role')\n this._isTransitioning = false\n\n this._backdrop.hide(() => {\n document.body.classList.remove(CLASS_NAME_OPEN)\n this._resetAdjustments()\n this._scrollBar.reset()\n EventHandler.trigger(this._element, EVENT_HIDDEN)\n })\n }\n\n _isAnimated() {\n return this._element.classList.contains(CLASS_NAME_FADE)\n }\n\n _triggerBackdropTransition() {\n const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n if (hideEvent.defaultPrevented) {\n return\n }\n\n const isModalOverflowing = this._element.scrollHeight > document.documentElement.clientHeight\n const initialOverflowY = this._element.style.overflowY\n // return if the following background transition hasn't yet completed\n if (initialOverflowY === 'hidden' || this._element.classList.contains(CLASS_NAME_STATIC)) {\n return\n }\n\n if (!isModalOverflowing) {\n this._element.style.overflowY = 'hidden'\n }\n\n this._element.classList.add(CLASS_NAME_STATIC)\n this._queueCallback(() => {\n this._element.classList.remove(CLASS_NAME_STATIC)\n this._queueCallback(() => {\n this._element.style.overflowY = initialOverflowY\n }, this._dialog)\n }, this._dialog)\n\n this._element.focus()\n }\n\n /**\n * The following methods are used to handle overflowing modals\n */\n\n _adjustDialog() {\n const isModalOverflowing = this._element.scrollHeight > document.documentElement.clientHeight\n const scrollbarWidth = this._scrollBar.getWidth()\n const isBodyOverflowing = scrollbarWidth > 0\n\n if (isBodyOverflowing && !isModalOverflowing) {\n const property = isRTL() ? 'paddingLeft' : 'paddingRight'\n this._element.style[property] = `${scrollbarWidth}px`\n }\n\n if (!isBodyOverflowing && isModalOverflowing) {\n const property = isRTL() ? 'paddingRight' : 'paddingLeft'\n this._element.style[property] = `${scrollbarWidth}px`\n }\n }\n\n _resetAdjustments() {\n this._element.style.paddingLeft = ''\n this._element.style.paddingRight = ''\n }\n\n // Static\n static jQueryInterface(config, relatedTarget) {\n return this.each(function () {\n const data = Modal.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config](relatedTarget)\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n const target = SelectorEngine.getElementFromSelector(this)\n\n if (['A', 'AREA'].includes(this.tagName)) {\n event.preventDefault()\n }\n\n EventHandler.one(target, EVENT_SHOW, showEvent => {\n if (showEvent.defaultPrevented) {\n // only register focus restorer if modal will actually get shown\n return\n }\n\n EventHandler.one(target, EVENT_HIDDEN, () => {\n if (isVisible(this)) {\n this.focus()\n }\n })\n })\n\n // avoid conflict when clicking modal toggler while another one is open\n const alreadyOpen = SelectorEngine.findOne(OPEN_SELECTOR)\n if (alreadyOpen) {\n Modal.getInstance(alreadyOpen).hide()\n }\n\n const data = Modal.getOrCreateInstance(target)\n\n data.toggle(this)\n})\n\nenableDismissTrigger(Modal)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Modal)\n\nexport default Modal\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap offcanvas.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport Backdrop from './util/backdrop.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport FocusTrap from './util/focustrap.js'\nimport {\n defineJQueryPlugin,\n isDisabled,\n isVisible\n} from './util/index.js'\nimport ScrollBarHelper from './util/scrollbar.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'offcanvas'\nconst DATA_KEY = 'bs.offcanvas'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\nconst ESCAPE_KEY = 'Escape'\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_SHOWING = 'showing'\nconst CLASS_NAME_HIDING = 'hiding'\nconst CLASS_NAME_BACKDROP = 'offcanvas-backdrop'\nconst OPEN_SELECTOR = '.offcanvas.show'\n\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDE_PREVENTED = `hidePrevented${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_RESIZE = `resize${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYDOWN_DISMISS = `keydown.dismiss${EVENT_KEY}`\n\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"offcanvas\"]'\n\nconst Default = {\n backdrop: true,\n keyboard: true,\n scroll: false\n}\n\nconst DefaultType = {\n backdrop: '(boolean|string)',\n keyboard: 'boolean',\n scroll: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Offcanvas extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._isShown = false\n this._backdrop = this._initializeBackDrop()\n this._focustrap = this._initializeFocusTrap()\n this._addEventListeners()\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n toggle(relatedTarget) {\n return this._isShown ? this.hide() : this.show(relatedTarget)\n }\n\n show(relatedTarget) {\n if (this._isShown) {\n return\n }\n\n const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, { relatedTarget })\n\n if (showEvent.defaultPrevented) {\n return\n }\n\n this._isShown = true\n this._backdrop.show()\n\n if (!this._config.scroll) {\n new ScrollBarHelper().hide()\n }\n\n this._element.setAttribute('aria-modal', true)\n this._element.setAttribute('role', 'dialog')\n this._element.classList.add(CLASS_NAME_SHOWING)\n\n const completeCallBack = () => {\n if (!this._config.scroll || this._config.backdrop) {\n this._focustrap.activate()\n }\n\n this._element.classList.add(CLASS_NAME_SHOW)\n this._element.classList.remove(CLASS_NAME_SHOWING)\n EventHandler.trigger(this._element, EVENT_SHOWN, { relatedTarget })\n }\n\n this._queueCallback(completeCallBack, this._element, true)\n }\n\n hide() {\n if (!this._isShown) {\n return\n }\n\n const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n if (hideEvent.defaultPrevented) {\n return\n }\n\n this._focustrap.deactivate()\n this._element.blur()\n this._isShown = false\n this._element.classList.add(CLASS_NAME_HIDING)\n this._backdrop.hide()\n\n const completeCallback = () => {\n this._element.classList.remove(CLASS_NAME_SHOW, CLASS_NAME_HIDING)\n this._element.removeAttribute('aria-modal')\n this._element.removeAttribute('role')\n\n if (!this._config.scroll) {\n new ScrollBarHelper().reset()\n }\n\n EventHandler.trigger(this._element, EVENT_HIDDEN)\n }\n\n this._queueCallback(completeCallback, this._element, true)\n }\n\n dispose() {\n this._backdrop.dispose()\n this._focustrap.deactivate()\n super.dispose()\n }\n\n // Private\n _initializeBackDrop() {\n const clickCallback = () => {\n if (this._config.backdrop === 'static') {\n EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n return\n }\n\n this.hide()\n }\n\n // 'static' option will be translated to true, and booleans will keep their value\n const isVisible = Boolean(this._config.backdrop)\n\n return new Backdrop({\n className: CLASS_NAME_BACKDROP,\n isVisible,\n isAnimated: true,\n rootElement: this._element.parentNode,\n clickCallback: isVisible ? clickCallback : null\n })\n }\n\n _initializeFocusTrap() {\n return new FocusTrap({\n trapElement: this._element\n })\n }\n\n _addEventListeners() {\n EventHandler.on(this._element, EVENT_KEYDOWN_DISMISS, event => {\n if (event.key !== ESCAPE_KEY) {\n return\n }\n\n if (this._config.keyboard) {\n this.hide()\n return\n }\n\n EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n })\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Offcanvas.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config](this)\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n const target = SelectorEngine.getElementFromSelector(this)\n\n if (['A', 'AREA'].includes(this.tagName)) {\n event.preventDefault()\n }\n\n if (isDisabled(this)) {\n return\n }\n\n EventHandler.one(target, EVENT_HIDDEN, () => {\n // focus on trigger when it is closed\n if (isVisible(this)) {\n this.focus()\n }\n })\n\n // avoid conflict when clicking a toggler of an offcanvas, while another is open\n const alreadyOpen = SelectorEngine.findOne(OPEN_SELECTOR)\n if (alreadyOpen && alreadyOpen !== target) {\n Offcanvas.getInstance(alreadyOpen).hide()\n }\n\n const data = Offcanvas.getOrCreateInstance(target)\n data.toggle(this)\n})\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n for (const selector of SelectorEngine.find(OPEN_SELECTOR)) {\n Offcanvas.getOrCreateInstance(selector).show()\n }\n})\n\nEventHandler.on(window, EVENT_RESIZE, () => {\n for (const element of SelectorEngine.find('[aria-modal][class*=show][class*=offcanvas-]')) {\n if (getComputedStyle(element).position !== 'fixed') {\n Offcanvas.getOrCreateInstance(element).hide()\n }\n }\n})\n\nenableDismissTrigger(Offcanvas)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Offcanvas)\n\nexport default Offcanvas\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/sanitizer.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\n// js-docs-start allow-list\nconst ARIA_ATTRIBUTE_PATTERN = /^aria-[\\w-]*$/i\n\nexport const DefaultAllowlist = {\n // Global attributes allowed on any supplied element below.\n '*': ['class', 'dir', 'id', 'lang', 'role', ARIA_ATTRIBUTE_PATTERN],\n a: ['target', 'href', 'title', 'rel'],\n area: [],\n b: [],\n br: [],\n col: [],\n code: [],\n div: [],\n em: [],\n hr: [],\n h1: [],\n h2: [],\n h3: [],\n h4: [],\n h5: [],\n h6: [],\n i: [],\n img: ['src', 'srcset', 'alt', 'title', 'width', 'height'],\n li: [],\n ol: [],\n p: [],\n pre: [],\n s: [],\n small: [],\n span: [],\n sub: [],\n sup: [],\n strong: [],\n u: [],\n ul: []\n}\n// js-docs-end allow-list\n\nconst uriAttributes = new Set([\n 'background',\n 'cite',\n 'href',\n 'itemtype',\n 'longdesc',\n 'poster',\n 'src',\n 'xlink:href'\n])\n\n/**\n * A pattern that recognizes URLs that are safe wrt. XSS in URL navigation\n * contexts.\n *\n * Shout-out to Angular https://github.com/angular/angular/blob/15.2.8/packages/core/src/sanitization/url_sanitizer.ts#L38\n */\n// eslint-disable-next-line unicorn/better-regex\nconst SAFE_URL_PATTERN = /^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i\n\nconst allowedAttribute = (attribute, allowedAttributeList) => {\n const attributeName = attribute.nodeName.toLowerCase()\n\n if (allowedAttributeList.includes(attributeName)) {\n if (uriAttributes.has(attributeName)) {\n return Boolean(SAFE_URL_PATTERN.test(attribute.nodeValue))\n }\n\n return true\n }\n\n // Check if a regular expression validates the attribute.\n return allowedAttributeList.filter(attributeRegex => attributeRegex instanceof RegExp)\n .some(regex => regex.test(attributeName))\n}\n\nexport function sanitizeHtml(unsafeHtml, allowList, sanitizeFunction) {\n if (!unsafeHtml.length) {\n return unsafeHtml\n }\n\n if (sanitizeFunction && typeof sanitizeFunction === 'function') {\n return sanitizeFunction(unsafeHtml)\n }\n\n const domParser = new window.DOMParser()\n const createdDocument = domParser.parseFromString(unsafeHtml, 'text/html')\n const elements = [].concat(...createdDocument.body.querySelectorAll('*'))\n\n for (const element of elements) {\n const elementName = element.nodeName.toLowerCase()\n\n if (!Object.keys(allowList).includes(elementName)) {\n element.remove()\n continue\n }\n\n const attributeList = [].concat(...element.attributes)\n const allowedAttributes = [].concat(allowList['*'] || [], allowList[elementName] || [])\n\n for (const attribute of attributeList) {\n if (!allowedAttribute(attribute, allowedAttributes)) {\n element.removeAttribute(attribute.nodeName)\n }\n }\n }\n\n return createdDocument.body.innerHTML\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/template-factory.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport SelectorEngine from '../dom/selector-engine.js'\nimport Config from './config.js'\nimport { DefaultAllowlist, sanitizeHtml } from './sanitizer.js'\nimport { execute, getElement, isElement } from './index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'TemplateFactory'\n\nconst Default = {\n allowList: DefaultAllowlist,\n content: {}, // { selector : text , selector2 : text2 , }\n extraClass: '',\n html: false,\n sanitize: true,\n sanitizeFn: null,\n template: '
    '\n}\n\nconst DefaultType = {\n allowList: 'object',\n content: 'object',\n extraClass: '(string|function)',\n html: 'boolean',\n sanitize: 'boolean',\n sanitizeFn: '(null|function)',\n template: 'string'\n}\n\nconst DefaultContentType = {\n entry: '(string|element|function|null)',\n selector: '(string|element)'\n}\n\n/**\n * Class definition\n */\n\nclass TemplateFactory extends Config {\n constructor(config) {\n super()\n this._config = this._getConfig(config)\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n getContent() {\n return Object.values(this._config.content)\n .map(config => this._resolvePossibleFunction(config))\n .filter(Boolean)\n }\n\n hasContent() {\n return this.getContent().length > 0\n }\n\n changeContent(content) {\n this._checkContent(content)\n this._config.content = { ...this._config.content, ...content }\n return this\n }\n\n toHtml() {\n const templateWrapper = document.createElement('div')\n templateWrapper.innerHTML = this._maybeSanitize(this._config.template)\n\n for (const [selector, text] of Object.entries(this._config.content)) {\n this._setContent(templateWrapper, text, selector)\n }\n\n const template = templateWrapper.children[0]\n const extraClass = this._resolvePossibleFunction(this._config.extraClass)\n\n if (extraClass) {\n template.classList.add(...extraClass.split(' '))\n }\n\n return template\n }\n\n // Private\n _typeCheckConfig(config) {\n super._typeCheckConfig(config)\n this._checkContent(config.content)\n }\n\n _checkContent(arg) {\n for (const [selector, content] of Object.entries(arg)) {\n super._typeCheckConfig({ selector, entry: content }, DefaultContentType)\n }\n }\n\n _setContent(template, content, selector) {\n const templateElement = SelectorEngine.findOne(selector, template)\n\n if (!templateElement) {\n return\n }\n\n content = this._resolvePossibleFunction(content)\n\n if (!content) {\n templateElement.remove()\n return\n }\n\n if (isElement(content)) {\n this._putElementInTemplate(getElement(content), templateElement)\n return\n }\n\n if (this._config.html) {\n templateElement.innerHTML = this._maybeSanitize(content)\n return\n }\n\n templateElement.textContent = content\n }\n\n _maybeSanitize(arg) {\n return this._config.sanitize ? sanitizeHtml(arg, this._config.allowList, this._config.sanitizeFn) : arg\n }\n\n _resolvePossibleFunction(arg) {\n return execute(arg, [this])\n }\n\n _putElementInTemplate(element, templateElement) {\n if (this._config.html) {\n templateElement.innerHTML = ''\n templateElement.append(element)\n return\n }\n\n templateElement.textContent = element.textContent\n }\n}\n\nexport default TemplateFactory\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap tooltip.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport * as Popper from '@popperjs/core'\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport Manipulator from './dom/manipulator.js'\nimport { defineJQueryPlugin, execute, findShadowRoot, getElement, getUID, isRTL, noop } from './util/index.js'\nimport { DefaultAllowlist } from './util/sanitizer.js'\nimport TemplateFactory from './util/template-factory.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'tooltip'\nconst DISALLOWED_ATTRIBUTES = new Set(['sanitize', 'allowList', 'sanitizeFn'])\n\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_MODAL = 'modal'\nconst CLASS_NAME_SHOW = 'show'\n\nconst SELECTOR_TOOLTIP_INNER = '.tooltip-inner'\nconst SELECTOR_MODAL = `.${CLASS_NAME_MODAL}`\n\nconst EVENT_MODAL_HIDE = 'hide.bs.modal'\n\nconst TRIGGER_HOVER = 'hover'\nconst TRIGGER_FOCUS = 'focus'\nconst TRIGGER_CLICK = 'click'\nconst TRIGGER_MANUAL = 'manual'\n\nconst EVENT_HIDE = 'hide'\nconst EVENT_HIDDEN = 'hidden'\nconst EVENT_SHOW = 'show'\nconst EVENT_SHOWN = 'shown'\nconst EVENT_INSERTED = 'inserted'\nconst EVENT_CLICK = 'click'\nconst EVENT_FOCUSIN = 'focusin'\nconst EVENT_FOCUSOUT = 'focusout'\nconst EVENT_MOUSEENTER = 'mouseenter'\nconst EVENT_MOUSELEAVE = 'mouseleave'\n\nconst AttachmentMap = {\n AUTO: 'auto',\n TOP: 'top',\n RIGHT: isRTL() ? 'left' : 'right',\n BOTTOM: 'bottom',\n LEFT: isRTL() ? 'right' : 'left'\n}\n\nconst Default = {\n allowList: DefaultAllowlist,\n animation: true,\n boundary: 'clippingParents',\n container: false,\n customClass: '',\n delay: 0,\n fallbackPlacements: ['top', 'right', 'bottom', 'left'],\n html: false,\n offset: [0, 6],\n placement: 'top',\n popperConfig: null,\n sanitize: true,\n sanitizeFn: null,\n selector: false,\n template: '
    ' +\n '
    ' +\n '
    ' +\n '
    ',\n title: '',\n trigger: 'hover focus'\n}\n\nconst DefaultType = {\n allowList: 'object',\n animation: 'boolean',\n boundary: '(string|element)',\n container: '(string|element|boolean)',\n customClass: '(string|function)',\n delay: '(number|object)',\n fallbackPlacements: 'array',\n html: 'boolean',\n offset: '(array|string|function)',\n placement: '(string|function)',\n popperConfig: '(null|object|function)',\n sanitize: 'boolean',\n sanitizeFn: '(null|function)',\n selector: '(string|boolean)',\n template: 'string',\n title: '(string|element|function)',\n trigger: 'string'\n}\n\n/**\n * Class definition\n */\n\nclass Tooltip extends BaseComponent {\n constructor(element, config) {\n if (typeof Popper === 'undefined') {\n throw new TypeError('Bootstrap\\'s tooltips require Popper (https://popper.js.org)')\n }\n\n super(element, config)\n\n // Private\n this._isEnabled = true\n this._timeout = 0\n this._isHovered = null\n this._activeTrigger = {}\n this._popper = null\n this._templateFactory = null\n this._newContent = null\n\n // Protected\n this.tip = null\n\n this._setListeners()\n\n if (!this._config.selector) {\n this._fixTitle()\n }\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n enable() {\n this._isEnabled = true\n }\n\n disable() {\n this._isEnabled = false\n }\n\n toggleEnabled() {\n this._isEnabled = !this._isEnabled\n }\n\n toggle() {\n if (!this._isEnabled) {\n return\n }\n\n this._activeTrigger.click = !this._activeTrigger.click\n if (this._isShown()) {\n this._leave()\n return\n }\n\n this._enter()\n }\n\n dispose() {\n clearTimeout(this._timeout)\n\n EventHandler.off(this._element.closest(SELECTOR_MODAL), EVENT_MODAL_HIDE, this._hideModalHandler)\n\n if (this._element.getAttribute('data-bs-original-title')) {\n this._element.setAttribute('title', this._element.getAttribute('data-bs-original-title'))\n }\n\n this._disposePopper()\n super.dispose()\n }\n\n show() {\n if (this._element.style.display === 'none') {\n throw new Error('Please use show on visible elements')\n }\n\n if (!(this._isWithContent() && this._isEnabled)) {\n return\n }\n\n const showEvent = EventHandler.trigger(this._element, this.constructor.eventName(EVENT_SHOW))\n const shadowRoot = findShadowRoot(this._element)\n const isInTheDom = (shadowRoot || this._element.ownerDocument.documentElement).contains(this._element)\n\n if (showEvent.defaultPrevented || !isInTheDom) {\n return\n }\n\n // TODO: v6 remove this or make it optional\n this._disposePopper()\n\n const tip = this._getTipElement()\n\n this._element.setAttribute('aria-describedby', tip.getAttribute('id'))\n\n const { container } = this._config\n\n if (!this._element.ownerDocument.documentElement.contains(this.tip)) {\n container.append(tip)\n EventHandler.trigger(this._element, this.constructor.eventName(EVENT_INSERTED))\n }\n\n this._popper = this._createPopper(tip)\n\n tip.classList.add(CLASS_NAME_SHOW)\n\n // If this is a touch-enabled device we add extra\n // empty mouseover listeners to the body's immediate children;\n // only needed because of broken event delegation on iOS\n // https://www.quirksmode.org/blog/archives/2014/02/mouse_event_bub.html\n if ('ontouchstart' in document.documentElement) {\n for (const element of [].concat(...document.body.children)) {\n EventHandler.on(element, 'mouseover', noop)\n }\n }\n\n const complete = () => {\n EventHandler.trigger(this._element, this.constructor.eventName(EVENT_SHOWN))\n\n if (this._isHovered === false) {\n this._leave()\n }\n\n this._isHovered = false\n }\n\n this._queueCallback(complete, this.tip, this._isAnimated())\n }\n\n hide() {\n if (!this._isShown()) {\n return\n }\n\n const hideEvent = EventHandler.trigger(this._element, this.constructor.eventName(EVENT_HIDE))\n if (hideEvent.defaultPrevented) {\n return\n }\n\n const tip = this._getTipElement()\n tip.classList.remove(CLASS_NAME_SHOW)\n\n // If this is a touch-enabled device we remove the extra\n // empty mouseover listeners we added for iOS support\n if ('ontouchstart' in document.documentElement) {\n for (const element of [].concat(...document.body.children)) {\n EventHandler.off(element, 'mouseover', noop)\n }\n }\n\n this._activeTrigger[TRIGGER_CLICK] = false\n this._activeTrigger[TRIGGER_FOCUS] = false\n this._activeTrigger[TRIGGER_HOVER] = false\n this._isHovered = null // it is a trick to support manual triggering\n\n const complete = () => {\n if (this._isWithActiveTrigger()) {\n return\n }\n\n if (!this._isHovered) {\n this._disposePopper()\n }\n\n this._element.removeAttribute('aria-describedby')\n EventHandler.trigger(this._element, this.constructor.eventName(EVENT_HIDDEN))\n }\n\n this._queueCallback(complete, this.tip, this._isAnimated())\n }\n\n update() {\n if (this._popper) {\n this._popper.update()\n }\n }\n\n // Protected\n _isWithContent() {\n return Boolean(this._getTitle())\n }\n\n _getTipElement() {\n if (!this.tip) {\n this.tip = this._createTipElement(this._newContent || this._getContentForTemplate())\n }\n\n return this.tip\n }\n\n _createTipElement(content) {\n const tip = this._getTemplateFactory(content).toHtml()\n\n // TODO: remove this check in v6\n if (!tip) {\n return null\n }\n\n tip.classList.remove(CLASS_NAME_FADE, CLASS_NAME_SHOW)\n // TODO: v6 the following can be achieved with CSS only\n tip.classList.add(`bs-${this.constructor.NAME}-auto`)\n\n const tipId = getUID(this.constructor.NAME).toString()\n\n tip.setAttribute('id', tipId)\n\n if (this._isAnimated()) {\n tip.classList.add(CLASS_NAME_FADE)\n }\n\n return tip\n }\n\n setContent(content) {\n this._newContent = content\n if (this._isShown()) {\n this._disposePopper()\n this.show()\n }\n }\n\n _getTemplateFactory(content) {\n if (this._templateFactory) {\n this._templateFactory.changeContent(content)\n } else {\n this._templateFactory = new TemplateFactory({\n ...this._config,\n // the `content` var has to be after `this._config`\n // to override config.content in case of popover\n content,\n extraClass: this._resolvePossibleFunction(this._config.customClass)\n })\n }\n\n return this._templateFactory\n }\n\n _getContentForTemplate() {\n return {\n [SELECTOR_TOOLTIP_INNER]: this._getTitle()\n }\n }\n\n _getTitle() {\n return this._resolvePossibleFunction(this._config.title) || this._element.getAttribute('data-bs-original-title')\n }\n\n // Private\n _initializeOnDelegatedTarget(event) {\n return this.constructor.getOrCreateInstance(event.delegateTarget, this._getDelegateConfig())\n }\n\n _isAnimated() {\n return this._config.animation || (this.tip && this.tip.classList.contains(CLASS_NAME_FADE))\n }\n\n _isShown() {\n return this.tip && this.tip.classList.contains(CLASS_NAME_SHOW)\n }\n\n _createPopper(tip) {\n const placement = execute(this._config.placement, [this, tip, this._element])\n const attachment = AttachmentMap[placement.toUpperCase()]\n return Popper.createPopper(this._element, tip, this._getPopperConfig(attachment))\n }\n\n _getOffset() {\n const { offset } = this._config\n\n if (typeof offset === 'string') {\n return offset.split(',').map(value => Number.parseInt(value, 10))\n }\n\n if (typeof offset === 'function') {\n return popperData => offset(popperData, this._element)\n }\n\n return offset\n }\n\n _resolvePossibleFunction(arg) {\n return execute(arg, [this._element])\n }\n\n _getPopperConfig(attachment) {\n const defaultBsPopperConfig = {\n placement: attachment,\n modifiers: [\n {\n name: 'flip',\n options: {\n fallbackPlacements: this._config.fallbackPlacements\n }\n },\n {\n name: 'offset',\n options: {\n offset: this._getOffset()\n }\n },\n {\n name: 'preventOverflow',\n options: {\n boundary: this._config.boundary\n }\n },\n {\n name: 'arrow',\n options: {\n element: `.${this.constructor.NAME}-arrow`\n }\n },\n {\n name: 'preSetPlacement',\n enabled: true,\n phase: 'beforeMain',\n fn: data => {\n // Pre-set Popper's placement attribute in order to read the arrow sizes properly.\n // Otherwise, Popper mixes up the width and height dimensions since the initial arrow style is for top placement\n this._getTipElement().setAttribute('data-popper-placement', data.state.placement)\n }\n }\n ]\n }\n\n return {\n ...defaultBsPopperConfig,\n ...execute(this._config.popperConfig, [defaultBsPopperConfig])\n }\n }\n\n _setListeners() {\n const triggers = this._config.trigger.split(' ')\n\n for (const trigger of triggers) {\n if (trigger === 'click') {\n EventHandler.on(this._element, this.constructor.eventName(EVENT_CLICK), this._config.selector, event => {\n const context = this._initializeOnDelegatedTarget(event)\n context.toggle()\n })\n } else if (trigger !== TRIGGER_MANUAL) {\n const eventIn = trigger === TRIGGER_HOVER ?\n this.constructor.eventName(EVENT_MOUSEENTER) :\n this.constructor.eventName(EVENT_FOCUSIN)\n const eventOut = trigger === TRIGGER_HOVER ?\n this.constructor.eventName(EVENT_MOUSELEAVE) :\n this.constructor.eventName(EVENT_FOCUSOUT)\n\n EventHandler.on(this._element, eventIn, this._config.selector, event => {\n const context = this._initializeOnDelegatedTarget(event)\n context._activeTrigger[event.type === 'focusin' ? TRIGGER_FOCUS : TRIGGER_HOVER] = true\n context._enter()\n })\n EventHandler.on(this._element, eventOut, this._config.selector, event => {\n const context = this._initializeOnDelegatedTarget(event)\n context._activeTrigger[event.type === 'focusout' ? TRIGGER_FOCUS : TRIGGER_HOVER] =\n context._element.contains(event.relatedTarget)\n\n context._leave()\n })\n }\n }\n\n this._hideModalHandler = () => {\n if (this._element) {\n this.hide()\n }\n }\n\n EventHandler.on(this._element.closest(SELECTOR_MODAL), EVENT_MODAL_HIDE, this._hideModalHandler)\n }\n\n _fixTitle() {\n const title = this._element.getAttribute('title')\n\n if (!title) {\n return\n }\n\n if (!this._element.getAttribute('aria-label') && !this._element.textContent.trim()) {\n this._element.setAttribute('aria-label', title)\n }\n\n this._element.setAttribute('data-bs-original-title', title) // DO NOT USE IT. Is only for backwards compatibility\n this._element.removeAttribute('title')\n }\n\n _enter() {\n if (this._isShown() || this._isHovered) {\n this._isHovered = true\n return\n }\n\n this._isHovered = true\n\n this._setTimeout(() => {\n if (this._isHovered) {\n this.show()\n }\n }, this._config.delay.show)\n }\n\n _leave() {\n if (this._isWithActiveTrigger()) {\n return\n }\n\n this._isHovered = false\n\n this._setTimeout(() => {\n if (!this._isHovered) {\n this.hide()\n }\n }, this._config.delay.hide)\n }\n\n _setTimeout(handler, timeout) {\n clearTimeout(this._timeout)\n this._timeout = setTimeout(handler, timeout)\n }\n\n _isWithActiveTrigger() {\n return Object.values(this._activeTrigger).includes(true)\n }\n\n _getConfig(config) {\n const dataAttributes = Manipulator.getDataAttributes(this._element)\n\n for (const dataAttribute of Object.keys(dataAttributes)) {\n if (DISALLOWED_ATTRIBUTES.has(dataAttribute)) {\n delete dataAttributes[dataAttribute]\n }\n }\n\n config = {\n ...dataAttributes,\n ...(typeof config === 'object' && config ? config : {})\n }\n config = this._mergeConfigObj(config)\n config = this._configAfterMerge(config)\n this._typeCheckConfig(config)\n return config\n }\n\n _configAfterMerge(config) {\n config.container = config.container === false ? document.body : getElement(config.container)\n\n if (typeof config.delay === 'number') {\n config.delay = {\n show: config.delay,\n hide: config.delay\n }\n }\n\n if (typeof config.title === 'number') {\n config.title = config.title.toString()\n }\n\n if (typeof config.content === 'number') {\n config.content = config.content.toString()\n }\n\n return config\n }\n\n _getDelegateConfig() {\n const config = {}\n\n for (const [key, value] of Object.entries(this._config)) {\n if (this.constructor.Default[key] !== value) {\n config[key] = value\n }\n }\n\n config.selector = false\n config.trigger = 'manual'\n\n // In the future can be replaced with:\n // const keysWithDifferentValues = Object.entries(this._config).filter(entry => this.constructor.Default[entry[0]] !== this._config[entry[0]])\n // `Object.fromEntries(keysWithDifferentValues)`\n return config\n }\n\n _disposePopper() {\n if (this._popper) {\n this._popper.destroy()\n this._popper = null\n }\n\n if (this.tip) {\n this.tip.remove()\n this.tip = null\n }\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Tooltip.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n })\n }\n}\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Tooltip)\n\nexport default Tooltip\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap popover.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Tooltip from './tooltip.js'\nimport { defineJQueryPlugin } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'popover'\n\nconst SELECTOR_TITLE = '.popover-header'\nconst SELECTOR_CONTENT = '.popover-body'\n\nconst Default = {\n ...Tooltip.Default,\n content: '',\n offset: [0, 8],\n placement: 'right',\n template: '
    ' +\n '
    ' +\n '

    ' +\n '
    ' +\n '
    ',\n trigger: 'click'\n}\n\nconst DefaultType = {\n ...Tooltip.DefaultType,\n content: '(null|string|element|function)'\n}\n\n/**\n * Class definition\n */\n\nclass Popover extends Tooltip {\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Overrides\n _isWithContent() {\n return this._getTitle() || this._getContent()\n }\n\n // Private\n _getContentForTemplate() {\n return {\n [SELECTOR_TITLE]: this._getTitle(),\n [SELECTOR_CONTENT]: this._getContent()\n }\n }\n\n _getContent() {\n return this._resolvePossibleFunction(this._config.content)\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Popover.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n })\n }\n}\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Popover)\n\nexport default Popover\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap scrollspy.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport { defineJQueryPlugin, getElement, isDisabled, isVisible } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'scrollspy'\nconst DATA_KEY = 'bs.scrollspy'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst EVENT_ACTIVATE = `activate${EVENT_KEY}`\nconst EVENT_CLICK = `click${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_DROPDOWN_ITEM = 'dropdown-item'\nconst CLASS_NAME_ACTIVE = 'active'\n\nconst SELECTOR_DATA_SPY = '[data-bs-spy=\"scroll\"]'\nconst SELECTOR_TARGET_LINKS = '[href]'\nconst SELECTOR_NAV_LIST_GROUP = '.nav, .list-group'\nconst SELECTOR_NAV_LINKS = '.nav-link'\nconst SELECTOR_NAV_ITEMS = '.nav-item'\nconst SELECTOR_LIST_ITEMS = '.list-group-item'\nconst SELECTOR_LINK_ITEMS = `${SELECTOR_NAV_LINKS}, ${SELECTOR_NAV_ITEMS} > ${SELECTOR_NAV_LINKS}, ${SELECTOR_LIST_ITEMS}`\nconst SELECTOR_DROPDOWN = '.dropdown'\nconst SELECTOR_DROPDOWN_TOGGLE = '.dropdown-toggle'\n\nconst Default = {\n offset: null, // TODO: v6 @deprecated, keep it for backwards compatibility reasons\n rootMargin: '0px 0px -25%',\n smoothScroll: false,\n target: null,\n threshold: [0.1, 0.5, 1]\n}\n\nconst DefaultType = {\n offset: '(number|null)', // TODO v6 @deprecated, keep it for backwards compatibility reasons\n rootMargin: 'string',\n smoothScroll: 'boolean',\n target: 'element',\n threshold: 'array'\n}\n\n/**\n * Class definition\n */\n\nclass ScrollSpy extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n // this._element is the observablesContainer and config.target the menu links wrapper\n this._targetLinks = new Map()\n this._observableSections = new Map()\n this._rootElement = getComputedStyle(this._element).overflowY === 'visible' ? null : this._element\n this._activeTarget = null\n this._observer = null\n this._previousScrollData = {\n visibleEntryTop: 0,\n parentScrollTop: 0\n }\n this.refresh() // initialize\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n refresh() {\n this._initializeTargetsAndObservables()\n this._maybeEnableSmoothScroll()\n\n if (this._observer) {\n this._observer.disconnect()\n } else {\n this._observer = this._getNewObserver()\n }\n\n for (const section of this._observableSections.values()) {\n this._observer.observe(section)\n }\n }\n\n dispose() {\n this._observer.disconnect()\n super.dispose()\n }\n\n // Private\n _configAfterMerge(config) {\n // TODO: on v6 target should be given explicitly & remove the {target: 'ss-target'} case\n config.target = getElement(config.target) || document.body\n\n // TODO: v6 Only for backwards compatibility reasons. Use rootMargin only\n config.rootMargin = config.offset ? `${config.offset}px 0px -30%` : config.rootMargin\n\n if (typeof config.threshold === 'string') {\n config.threshold = config.threshold.split(',').map(value => Number.parseFloat(value))\n }\n\n return config\n }\n\n _maybeEnableSmoothScroll() {\n if (!this._config.smoothScroll) {\n return\n }\n\n // unregister any previous listeners\n EventHandler.off(this._config.target, EVENT_CLICK)\n\n EventHandler.on(this._config.target, EVENT_CLICK, SELECTOR_TARGET_LINKS, event => {\n const observableSection = this._observableSections.get(event.target.hash)\n if (observableSection) {\n event.preventDefault()\n const root = this._rootElement || window\n const height = observableSection.offsetTop - this._element.offsetTop\n if (root.scrollTo) {\n root.scrollTo({ top: height, behavior: 'smooth' })\n return\n }\n\n // Chrome 60 doesn't support `scrollTo`\n root.scrollTop = height\n }\n })\n }\n\n _getNewObserver() {\n const options = {\n root: this._rootElement,\n threshold: this._config.threshold,\n rootMargin: this._config.rootMargin\n }\n\n return new IntersectionObserver(entries => this._observerCallback(entries), options)\n }\n\n // The logic of selection\n _observerCallback(entries) {\n const targetElement = entry => this._targetLinks.get(`#${entry.target.id}`)\n const activate = entry => {\n this._previousScrollData.visibleEntryTop = entry.target.offsetTop\n this._process(targetElement(entry))\n }\n\n const parentScrollTop = (this._rootElement || document.documentElement).scrollTop\n const userScrollsDown = parentScrollTop >= this._previousScrollData.parentScrollTop\n this._previousScrollData.parentScrollTop = parentScrollTop\n\n for (const entry of entries) {\n if (!entry.isIntersecting) {\n this._activeTarget = null\n this._clearActiveClass(targetElement(entry))\n\n continue\n }\n\n const entryIsLowerThanPrevious = entry.target.offsetTop >= this._previousScrollData.visibleEntryTop\n // if we are scrolling down, pick the bigger offsetTop\n if (userScrollsDown && entryIsLowerThanPrevious) {\n activate(entry)\n // if parent isn't scrolled, let's keep the first visible item, breaking the iteration\n if (!parentScrollTop) {\n return\n }\n\n continue\n }\n\n // if we are scrolling up, pick the smallest offsetTop\n if (!userScrollsDown && !entryIsLowerThanPrevious) {\n activate(entry)\n }\n }\n }\n\n _initializeTargetsAndObservables() {\n this._targetLinks = new Map()\n this._observableSections = new Map()\n\n const targetLinks = SelectorEngine.find(SELECTOR_TARGET_LINKS, this._config.target)\n\n for (const anchor of targetLinks) {\n // ensure that the anchor has an id and is not disabled\n if (!anchor.hash || isDisabled(anchor)) {\n continue\n }\n\n const observableSection = SelectorEngine.findOne(decodeURI(anchor.hash), this._element)\n\n // ensure that the observableSection exists & is visible\n if (isVisible(observableSection)) {\n this._targetLinks.set(decodeURI(anchor.hash), anchor)\n this._observableSections.set(anchor.hash, observableSection)\n }\n }\n }\n\n _process(target) {\n if (this._activeTarget === target) {\n return\n }\n\n this._clearActiveClass(this._config.target)\n this._activeTarget = target\n target.classList.add(CLASS_NAME_ACTIVE)\n this._activateParents(target)\n\n EventHandler.trigger(this._element, EVENT_ACTIVATE, { relatedTarget: target })\n }\n\n _activateParents(target) {\n // Activate dropdown parents\n if (target.classList.contains(CLASS_NAME_DROPDOWN_ITEM)) {\n SelectorEngine.findOne(SELECTOR_DROPDOWN_TOGGLE, target.closest(SELECTOR_DROPDOWN))\n .classList.add(CLASS_NAME_ACTIVE)\n return\n }\n\n for (const listGroup of SelectorEngine.parents(target, SELECTOR_NAV_LIST_GROUP)) {\n // Set triggered links parents as active\n // With both
      and
    ')},createChildNavList:function(e){var t=this.createNavList();return e.append(t),t},generateNavEl:function(e,t){var n=a('
    ');n.attr("href","#"+e),n.text(t);var r=a("
  • ");return r.append(n),r},generateNavItem:function(e){var t=this.generateAnchor(e),n=a(e),r=n.data("toc-text")||n.text();return this.generateNavEl(t,r)},getTopLevel:function(e){for(var t=1;t<=6;t++){if(1 + + + + + + + + + + + + diff --git a/deps/font-awesome-6.4.2/css/all.css b/deps/font-awesome-6.4.2/css/all.css new file mode 100644 index 00000000..bdb6e3ae --- /dev/null +++ b/deps/font-awesome-6.4.2/css/all.css @@ -0,0 +1,7968 @@ +/*! + * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com + * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) + * Copyright 2023 Fonticons, Inc. + */ +.fa { + font-family: var(--fa-style-family, "Font Awesome 6 Free"); + font-weight: var(--fa-style, 900); } + +.fa, +.fa-classic, +.fa-sharp, +.fas, +.fa-solid, +.far, +.fa-regular, +.fab, +.fa-brands { + -moz-osx-font-smoothing: grayscale; + -webkit-font-smoothing: antialiased; + display: var(--fa-display, inline-block); + font-style: normal; + font-variant: normal; + line-height: 1; + text-rendering: auto; } + +.fas, +.fa-classic, +.fa-solid, +.far, +.fa-regular { + font-family: 'Font Awesome 6 Free'; } + +.fab, +.fa-brands { + font-family: 'Font Awesome 6 Brands'; } + +.fa-1x { + font-size: 1em; } + +.fa-2x { + font-size: 2em; } + +.fa-3x { + font-size: 3em; } + +.fa-4x { + font-size: 4em; } + +.fa-5x { + font-size: 5em; } + +.fa-6x { + font-size: 6em; } + +.fa-7x { + font-size: 7em; } + +.fa-8x { + font-size: 8em; } + +.fa-9x { + font-size: 9em; } + +.fa-10x { + font-size: 10em; } + +.fa-2xs { + font-size: 0.625em; + line-height: 0.1em; + vertical-align: 0.225em; } + +.fa-xs { + font-size: 0.75em; + line-height: 0.08333em; + vertical-align: 0.125em; } + +.fa-sm { + font-size: 0.875em; + line-height: 0.07143em; + vertical-align: 0.05357em; } + +.fa-lg { + font-size: 1.25em; + line-height: 0.05em; + vertical-align: -0.075em; } + +.fa-xl { + font-size: 1.5em; + line-height: 0.04167em; + vertical-align: -0.125em; } + +.fa-2xl { + font-size: 2em; + line-height: 0.03125em; + vertical-align: -0.1875em; } + +.fa-fw { + text-align: center; + width: 1.25em; } + +.fa-ul { + list-style-type: none; + margin-left: var(--fa-li-margin, 2.5em); + padding-left: 0; } + .fa-ul > li { + position: relative; } + +.fa-li { + left: calc(var(--fa-li-width, 2em) * -1); + position: absolute; + text-align: center; + width: var(--fa-li-width, 2em); + line-height: inherit; } + +.fa-border { + border-color: var(--fa-border-color, #eee); + border-radius: var(--fa-border-radius, 0.1em); + border-style: var(--fa-border-style, solid); + border-width: var(--fa-border-width, 0.08em); + padding: var(--fa-border-padding, 0.2em 0.25em 0.15em); } + +.fa-pull-left { + float: left; + margin-right: var(--fa-pull-margin, 0.3em); } + +.fa-pull-right { + float: right; + margin-left: var(--fa-pull-margin, 0.3em); } + +.fa-beat { + -webkit-animation-name: fa-beat; + animation-name: fa-beat; + -webkit-animation-delay: var(--fa-animation-delay, 0s); + animation-delay: var(--fa-animation-delay, 0s); + -webkit-animation-direction: var(--fa-animation-direction, normal); + animation-direction: var(--fa-animation-direction, normal); + -webkit-animation-duration: var(--fa-animation-duration, 1s); + animation-duration: var(--fa-animation-duration, 1s); + -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite); + animation-iteration-count: var(--fa-animation-iteration-count, infinite); + -webkit-animation-timing-function: var(--fa-animation-timing, ease-in-out); + animation-timing-function: var(--fa-animation-timing, ease-in-out); } + +.fa-bounce { + -webkit-animation-name: fa-bounce; + animation-name: fa-bounce; + -webkit-animation-delay: var(--fa-animation-delay, 0s); + animation-delay: var(--fa-animation-delay, 0s); + -webkit-animation-direction: var(--fa-animation-direction, normal); + animation-direction: var(--fa-animation-direction, normal); + -webkit-animation-duration: var(--fa-animation-duration, 1s); + animation-duration: var(--fa-animation-duration, 1s); + -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite); + animation-iteration-count: var(--fa-animation-iteration-count, infinite); + -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.28, 0.84, 0.42, 1)); + animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.28, 0.84, 0.42, 1)); } + +.fa-fade { + -webkit-animation-name: fa-fade; + animation-name: fa-fade; + -webkit-animation-delay: var(--fa-animation-delay, 0s); + animation-delay: var(--fa-animation-delay, 0s); + -webkit-animation-direction: var(--fa-animation-direction, normal); + animation-direction: var(--fa-animation-direction, normal); + -webkit-animation-duration: var(--fa-animation-duration, 1s); + animation-duration: var(--fa-animation-duration, 1s); + -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite); + animation-iteration-count: var(--fa-animation-iteration-count, infinite); + -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1)); + animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1)); } + +.fa-beat-fade { + -webkit-animation-name: fa-beat-fade; + animation-name: fa-beat-fade; + -webkit-animation-delay: var(--fa-animation-delay, 0s); + animation-delay: var(--fa-animation-delay, 0s); + -webkit-animation-direction: var(--fa-animation-direction, normal); + animation-direction: var(--fa-animation-direction, normal); + -webkit-animation-duration: var(--fa-animation-duration, 1s); + animation-duration: var(--fa-animation-duration, 1s); + -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite); + animation-iteration-count: var(--fa-animation-iteration-count, infinite); + -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1)); + animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1)); } + +.fa-flip { + -webkit-animation-name: fa-flip; + animation-name: fa-flip; + -webkit-animation-delay: var(--fa-animation-delay, 0s); + animation-delay: var(--fa-animation-delay, 0s); + -webkit-animation-direction: var(--fa-animation-direction, normal); + animation-direction: var(--fa-animation-direction, normal); + -webkit-animation-duration: var(--fa-animation-duration, 1s); + animation-duration: var(--fa-animation-duration, 1s); + -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite); + animation-iteration-count: var(--fa-animation-iteration-count, infinite); + -webkit-animation-timing-function: var(--fa-animation-timing, ease-in-out); + animation-timing-function: var(--fa-animation-timing, ease-in-out); } + +.fa-shake { + -webkit-animation-name: fa-shake; + animation-name: fa-shake; + -webkit-animation-delay: var(--fa-animation-delay, 0s); + animation-delay: var(--fa-animation-delay, 0s); + -webkit-animation-direction: var(--fa-animation-direction, normal); + animation-direction: var(--fa-animation-direction, normal); + -webkit-animation-duration: var(--fa-animation-duration, 1s); + animation-duration: var(--fa-animation-duration, 1s); + -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite); + animation-iteration-count: var(--fa-animation-iteration-count, infinite); + -webkit-animation-timing-function: var(--fa-animation-timing, linear); + animation-timing-function: var(--fa-animation-timing, linear); } + +.fa-spin { + -webkit-animation-name: fa-spin; + animation-name: fa-spin; + -webkit-animation-delay: var(--fa-animation-delay, 0s); + animation-delay: var(--fa-animation-delay, 0s); + -webkit-animation-direction: var(--fa-animation-direction, normal); + animation-direction: var(--fa-animation-direction, normal); + -webkit-animation-duration: var(--fa-animation-duration, 2s); + animation-duration: var(--fa-animation-duration, 2s); + -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite); + animation-iteration-count: var(--fa-animation-iteration-count, infinite); + -webkit-animation-timing-function: var(--fa-animation-timing, linear); + animation-timing-function: var(--fa-animation-timing, linear); } + +.fa-spin-reverse { + --fa-animation-direction: reverse; } + +.fa-pulse, +.fa-spin-pulse { + -webkit-animation-name: fa-spin; + animation-name: fa-spin; + -webkit-animation-direction: var(--fa-animation-direction, normal); + animation-direction: var(--fa-animation-direction, normal); + -webkit-animation-duration: var(--fa-animation-duration, 1s); + animation-duration: var(--fa-animation-duration, 1s); + -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite); + animation-iteration-count: var(--fa-animation-iteration-count, infinite); + -webkit-animation-timing-function: var(--fa-animation-timing, steps(8)); + animation-timing-function: var(--fa-animation-timing, steps(8)); } + +@media (prefers-reduced-motion: reduce) { + .fa-beat, + .fa-bounce, + .fa-fade, + .fa-beat-fade, + .fa-flip, + .fa-pulse, + .fa-shake, + .fa-spin, + .fa-spin-pulse { + -webkit-animation-delay: -1ms; + animation-delay: -1ms; + -webkit-animation-duration: 1ms; + animation-duration: 1ms; + -webkit-animation-iteration-count: 1; + animation-iteration-count: 1; + -webkit-transition-delay: 0s; + transition-delay: 0s; + -webkit-transition-duration: 0s; + transition-duration: 0s; } } + +@-webkit-keyframes fa-beat { + 0%, 90% { + -webkit-transform: scale(1); + transform: scale(1); } + 45% { + -webkit-transform: scale(var(--fa-beat-scale, 1.25)); + transform: scale(var(--fa-beat-scale, 1.25)); } } + +@keyframes fa-beat { + 0%, 90% { + -webkit-transform: scale(1); + transform: scale(1); } + 45% { + -webkit-transform: scale(var(--fa-beat-scale, 1.25)); + transform: scale(var(--fa-beat-scale, 1.25)); } } + +@-webkit-keyframes fa-bounce { + 0% { + -webkit-transform: scale(1, 1) translateY(0); + transform: scale(1, 1) translateY(0); } + 10% { + -webkit-transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0); + transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0); } + 30% { + -webkit-transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em)); + transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em)); } + 50% { + -webkit-transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0); + transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0); } + 57% { + -webkit-transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em)); + transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em)); } + 64% { + -webkit-transform: scale(1, 1) translateY(0); + transform: scale(1, 1) translateY(0); } + 100% { + -webkit-transform: scale(1, 1) translateY(0); + transform: scale(1, 1) translateY(0); } } + +@keyframes fa-bounce { + 0% { + -webkit-transform: scale(1, 1) translateY(0); + transform: scale(1, 1) translateY(0); } + 10% { + -webkit-transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0); + transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0); } + 30% { + -webkit-transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em)); + transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em)); } + 50% { + -webkit-transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0); + transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0); } + 57% { + -webkit-transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em)); + transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em)); } + 64% { + -webkit-transform: scale(1, 1) translateY(0); + transform: scale(1, 1) translateY(0); } + 100% { + -webkit-transform: scale(1, 1) translateY(0); + transform: scale(1, 1) translateY(0); } } + +@-webkit-keyframes fa-fade { + 50% { + opacity: var(--fa-fade-opacity, 0.4); } } + +@keyframes fa-fade { + 50% { + opacity: var(--fa-fade-opacity, 0.4); } } + +@-webkit-keyframes fa-beat-fade { + 0%, 100% { + opacity: var(--fa-beat-fade-opacity, 0.4); + -webkit-transform: scale(1); + transform: scale(1); } + 50% { + opacity: 1; + -webkit-transform: scale(var(--fa-beat-fade-scale, 1.125)); + transform: scale(var(--fa-beat-fade-scale, 1.125)); } } + +@keyframes fa-beat-fade { + 0%, 100% { + opacity: var(--fa-beat-fade-opacity, 0.4); + -webkit-transform: scale(1); + transform: scale(1); } + 50% { + opacity: 1; + -webkit-transform: scale(var(--fa-beat-fade-scale, 1.125)); + transform: scale(var(--fa-beat-fade-scale, 1.125)); } } + +@-webkit-keyframes fa-flip { + 50% { + -webkit-transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg)); + transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg)); } } + +@keyframes fa-flip { + 50% { + -webkit-transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg)); + transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg)); } } + +@-webkit-keyframes fa-shake { + 0% { + -webkit-transform: rotate(-15deg); + transform: rotate(-15deg); } + 4% { + -webkit-transform: rotate(15deg); + transform: rotate(15deg); } + 8%, 24% { + -webkit-transform: rotate(-18deg); + transform: rotate(-18deg); } + 12%, 28% { + -webkit-transform: rotate(18deg); + transform: rotate(18deg); } + 16% { + -webkit-transform: rotate(-22deg); + transform: rotate(-22deg); } + 20% { + -webkit-transform: rotate(22deg); + transform: rotate(22deg); } + 32% { + -webkit-transform: rotate(-12deg); + transform: rotate(-12deg); } + 36% { + -webkit-transform: rotate(12deg); + transform: rotate(12deg); } + 40%, 100% { + -webkit-transform: rotate(0deg); + transform: rotate(0deg); } } + +@keyframes fa-shake { + 0% { + -webkit-transform: rotate(-15deg); + transform: rotate(-15deg); } + 4% { + -webkit-transform: rotate(15deg); + transform: rotate(15deg); } + 8%, 24% { + -webkit-transform: rotate(-18deg); + transform: rotate(-18deg); } + 12%, 28% { + -webkit-transform: rotate(18deg); + transform: rotate(18deg); } + 16% { + -webkit-transform: rotate(-22deg); + transform: rotate(-22deg); } + 20% { + -webkit-transform: rotate(22deg); + transform: rotate(22deg); } + 32% { + -webkit-transform: rotate(-12deg); + transform: rotate(-12deg); } + 36% { + -webkit-transform: rotate(12deg); + transform: rotate(12deg); } + 40%, 100% { + -webkit-transform: rotate(0deg); + transform: rotate(0deg); } } + +@-webkit-keyframes fa-spin { + 0% { + -webkit-transform: rotate(0deg); + transform: rotate(0deg); } + 100% { + -webkit-transform: rotate(360deg); + transform: rotate(360deg); } } + +@keyframes fa-spin { + 0% { + -webkit-transform: rotate(0deg); + transform: rotate(0deg); } + 100% { + -webkit-transform: rotate(360deg); + transform: rotate(360deg); } } + +.fa-rotate-90 { + -webkit-transform: rotate(90deg); + transform: rotate(90deg); } + +.fa-rotate-180 { + -webkit-transform: rotate(180deg); + transform: rotate(180deg); } + +.fa-rotate-270 { + -webkit-transform: rotate(270deg); + transform: rotate(270deg); } + +.fa-flip-horizontal { + -webkit-transform: scale(-1, 1); + transform: scale(-1, 1); } + +.fa-flip-vertical { + -webkit-transform: scale(1, -1); + transform: scale(1, -1); } + +.fa-flip-both, +.fa-flip-horizontal.fa-flip-vertical { + -webkit-transform: scale(-1, -1); + transform: scale(-1, -1); } + +.fa-rotate-by { + -webkit-transform: rotate(var(--fa-rotate-angle, none)); + transform: rotate(var(--fa-rotate-angle, none)); } + +.fa-stack { + display: inline-block; + height: 2em; + line-height: 2em; + position: relative; + vertical-align: middle; + width: 2.5em; } + +.fa-stack-1x, +.fa-stack-2x { + left: 0; + position: absolute; + text-align: center; + width: 100%; + z-index: var(--fa-stack-z-index, auto); } + +.fa-stack-1x { + line-height: inherit; } + +.fa-stack-2x { + font-size: 2em; } + +.fa-inverse { + color: var(--fa-inverse, #fff); } + +/* Font Awesome uses the Unicode Private Use Area (PUA) to ensure screen +readers do not read off random characters that represent icons */ + +.fa-0::before { + content: "\30"; } + +.fa-1::before { + content: "\31"; } + +.fa-2::before { + content: "\32"; } + +.fa-3::before { + content: "\33"; } + +.fa-4::before { + content: "\34"; } + +.fa-5::before { + content: "\35"; } + +.fa-6::before { + content: "\36"; } + +.fa-7::before { + content: "\37"; } + +.fa-8::before { + content: "\38"; } + +.fa-9::before { + content: "\39"; } + +.fa-fill-drip::before { + content: "\f576"; } + +.fa-arrows-to-circle::before { + content: "\e4bd"; } + +.fa-circle-chevron-right::before { + content: "\f138"; } + +.fa-chevron-circle-right::before { + content: "\f138"; } + +.fa-at::before { + content: "\40"; } + +.fa-trash-can::before { + content: "\f2ed"; } + +.fa-trash-alt::before { + content: "\f2ed"; } + +.fa-text-height::before { + content: "\f034"; } + +.fa-user-xmark::before { + content: "\f235"; } + +.fa-user-times::before { + content: "\f235"; } + +.fa-stethoscope::before { + content: "\f0f1"; } + +.fa-message::before { + content: "\f27a"; } + +.fa-comment-alt::before { + content: "\f27a"; } + +.fa-info::before { + content: "\f129"; } + +.fa-down-left-and-up-right-to-center::before { + content: "\f422"; } + +.fa-compress-alt::before { + content: "\f422"; } + +.fa-explosion::before { + content: "\e4e9"; } + +.fa-file-lines::before { + content: "\f15c"; } + +.fa-file-alt::before { + content: "\f15c"; } + +.fa-file-text::before { + content: "\f15c"; } + +.fa-wave-square::before { + content: "\f83e"; } + +.fa-ring::before { + content: "\f70b"; } + +.fa-building-un::before { + content: "\e4d9"; } + +.fa-dice-three::before { + content: "\f527"; } + +.fa-calendar-days::before { + content: "\f073"; } + +.fa-calendar-alt::before { + content: "\f073"; } + +.fa-anchor-circle-check::before { + content: "\e4aa"; } + +.fa-building-circle-arrow-right::before { + content: "\e4d1"; } + +.fa-volleyball::before { + content: "\f45f"; } + +.fa-volleyball-ball::before { + content: "\f45f"; } + +.fa-arrows-up-to-line::before { + content: "\e4c2"; } + +.fa-sort-down::before { + content: "\f0dd"; } + +.fa-sort-desc::before { + content: "\f0dd"; } + +.fa-circle-minus::before { + content: "\f056"; } + +.fa-minus-circle::before { + content: "\f056"; } + +.fa-door-open::before { + content: "\f52b"; } + +.fa-right-from-bracket::before { + content: "\f2f5"; } + +.fa-sign-out-alt::before { + content: "\f2f5"; } + +.fa-atom::before { + content: "\f5d2"; } + +.fa-soap::before { + content: "\e06e"; } + +.fa-icons::before { + content: "\f86d"; } + +.fa-heart-music-camera-bolt::before { + content: "\f86d"; } + +.fa-microphone-lines-slash::before { + content: "\f539"; } + +.fa-microphone-alt-slash::before { + content: "\f539"; } + +.fa-bridge-circle-check::before { + content: "\e4c9"; } + +.fa-pump-medical::before { + content: "\e06a"; } + +.fa-fingerprint::before { + content: "\f577"; } + +.fa-hand-point-right::before { + content: "\f0a4"; } + +.fa-magnifying-glass-location::before { + content: "\f689"; } + +.fa-search-location::before { + content: "\f689"; } + +.fa-forward-step::before { + content: "\f051"; } + +.fa-step-forward::before { + content: "\f051"; } + +.fa-face-smile-beam::before { + content: "\f5b8"; } + +.fa-smile-beam::before { + content: "\f5b8"; } + +.fa-flag-checkered::before { + content: "\f11e"; } + +.fa-football::before { + content: "\f44e"; } + +.fa-football-ball::before { + content: "\f44e"; } + +.fa-school-circle-exclamation::before { + content: "\e56c"; } + +.fa-crop::before { + content: "\f125"; } + +.fa-angles-down::before { + content: "\f103"; } + +.fa-angle-double-down::before { + content: "\f103"; } + +.fa-users-rectangle::before { + content: "\e594"; } + +.fa-people-roof::before { + content: "\e537"; } + +.fa-people-line::before { + content: "\e534"; } + +.fa-beer-mug-empty::before { + content: "\f0fc"; } + +.fa-beer::before { + content: "\f0fc"; } + +.fa-diagram-predecessor::before { + content: "\e477"; } + +.fa-arrow-up-long::before { + content: "\f176"; } + +.fa-long-arrow-up::before { + content: "\f176"; } + +.fa-fire-flame-simple::before { + content: "\f46a"; } + +.fa-burn::before { + content: "\f46a"; } + +.fa-person::before { + content: "\f183"; } + +.fa-male::before { + content: "\f183"; } + +.fa-laptop::before { + content: "\f109"; } + +.fa-file-csv::before { + content: "\f6dd"; } + +.fa-menorah::before { + content: "\f676"; } + +.fa-truck-plane::before { + content: "\e58f"; } + +.fa-record-vinyl::before { + content: "\f8d9"; } + +.fa-face-grin-stars::before { + content: "\f587"; } + +.fa-grin-stars::before { + content: "\f587"; } + +.fa-bong::before { + content: "\f55c"; } + +.fa-spaghetti-monster-flying::before { + content: "\f67b"; } + +.fa-pastafarianism::before { + content: "\f67b"; } + +.fa-arrow-down-up-across-line::before { + content: "\e4af"; } + +.fa-spoon::before { + content: "\f2e5"; } + +.fa-utensil-spoon::before { + content: "\f2e5"; } + +.fa-jar-wheat::before { + content: "\e517"; } + +.fa-envelopes-bulk::before { + content: "\f674"; } + +.fa-mail-bulk::before { + content: "\f674"; } + +.fa-file-circle-exclamation::before { + content: "\e4eb"; } + +.fa-circle-h::before { + content: "\f47e"; } + +.fa-hospital-symbol::before { + content: "\f47e"; } + +.fa-pager::before { + content: "\f815"; } + +.fa-address-book::before { + content: "\f2b9"; } + +.fa-contact-book::before { + content: "\f2b9"; } + +.fa-strikethrough::before { + content: "\f0cc"; } + +.fa-k::before { + content: "\4b"; } + +.fa-landmark-flag::before { + content: "\e51c"; } + +.fa-pencil::before { + content: "\f303"; } + +.fa-pencil-alt::before { + content: "\f303"; } + +.fa-backward::before { + content: "\f04a"; } + +.fa-caret-right::before { + content: "\f0da"; } + +.fa-comments::before { + content: "\f086"; } + +.fa-paste::before { + content: "\f0ea"; } + +.fa-file-clipboard::before { + content: "\f0ea"; } + +.fa-code-pull-request::before { + content: "\e13c"; } + +.fa-clipboard-list::before { + content: "\f46d"; } + +.fa-truck-ramp-box::before { + content: "\f4de"; } + +.fa-truck-loading::before { + content: "\f4de"; } + +.fa-user-check::before { + content: "\f4fc"; } + +.fa-vial-virus::before { + content: "\e597"; } + +.fa-sheet-plastic::before { + content: "\e571"; } + +.fa-blog::before { + content: "\f781"; } + +.fa-user-ninja::before { + content: "\f504"; } + +.fa-person-arrow-up-from-line::before { + content: "\e539"; } + +.fa-scroll-torah::before { + content: "\f6a0"; } + +.fa-torah::before { + content: "\f6a0"; } + +.fa-broom-ball::before { + content: "\f458"; } + +.fa-quidditch::before { + content: "\f458"; } + +.fa-quidditch-broom-ball::before { + content: "\f458"; } + +.fa-toggle-off::before { + content: "\f204"; } + +.fa-box-archive::before { + content: "\f187"; } + +.fa-archive::before { + content: "\f187"; } + +.fa-person-drowning::before { + content: "\e545"; } + +.fa-arrow-down-9-1::before { + content: "\f886"; } + +.fa-sort-numeric-desc::before { + content: "\f886"; } + +.fa-sort-numeric-down-alt::before { + content: "\f886"; } + +.fa-face-grin-tongue-squint::before { + content: "\f58a"; } + +.fa-grin-tongue-squint::before { + content: "\f58a"; } + +.fa-spray-can::before { + content: "\f5bd"; } + +.fa-truck-monster::before { + content: "\f63b"; } + +.fa-w::before { + content: "\57"; } + +.fa-earth-africa::before { + content: "\f57c"; } + +.fa-globe-africa::before { + content: "\f57c"; } + +.fa-rainbow::before { + content: "\f75b"; } + +.fa-circle-notch::before { + content: "\f1ce"; } + +.fa-tablet-screen-button::before { + content: "\f3fa"; } + +.fa-tablet-alt::before { + content: "\f3fa"; } + +.fa-paw::before { + content: "\f1b0"; } + +.fa-cloud::before { + content: "\f0c2"; } + +.fa-trowel-bricks::before { + content: "\e58a"; } + +.fa-face-flushed::before { + content: "\f579"; } + +.fa-flushed::before { + content: "\f579"; } + +.fa-hospital-user::before { + content: "\f80d"; } + +.fa-tent-arrow-left-right::before { + content: "\e57f"; } + +.fa-gavel::before { + content: "\f0e3"; } + +.fa-legal::before { + content: "\f0e3"; } + +.fa-binoculars::before { + content: "\f1e5"; } + +.fa-microphone-slash::before { + content: "\f131"; } + +.fa-box-tissue::before { + content: "\e05b"; } + +.fa-motorcycle::before { + content: "\f21c"; } + +.fa-bell-concierge::before { + content: "\f562"; } + +.fa-concierge-bell::before { + content: "\f562"; } + +.fa-pen-ruler::before { + content: "\f5ae"; } + +.fa-pencil-ruler::before { + content: "\f5ae"; } + +.fa-people-arrows::before { + content: "\e068"; } + +.fa-people-arrows-left-right::before { + content: "\e068"; } + +.fa-mars-and-venus-burst::before { + content: "\e523"; } + +.fa-square-caret-right::before { + content: "\f152"; } + +.fa-caret-square-right::before { + content: "\f152"; } + +.fa-scissors::before { + content: "\f0c4"; } + +.fa-cut::before { + content: "\f0c4"; } + +.fa-sun-plant-wilt::before { + content: "\e57a"; } + +.fa-toilets-portable::before { + content: "\e584"; } + +.fa-hockey-puck::before { + content: "\f453"; } + +.fa-table::before { + content: "\f0ce"; } + +.fa-magnifying-glass-arrow-right::before { + content: "\e521"; } + +.fa-tachograph-digital::before { + content: "\f566"; } + +.fa-digital-tachograph::before { + content: "\f566"; } + +.fa-users-slash::before { + content: "\e073"; } + +.fa-clover::before { + content: "\e139"; } + +.fa-reply::before { + content: "\f3e5"; } + +.fa-mail-reply::before { + content: "\f3e5"; } + +.fa-star-and-crescent::before { + content: "\f699"; } + +.fa-house-fire::before { + content: "\e50c"; } + +.fa-square-minus::before { + content: "\f146"; } + +.fa-minus-square::before { + content: "\f146"; } + +.fa-helicopter::before { + content: "\f533"; } + +.fa-compass::before { + content: "\f14e"; } + +.fa-square-caret-down::before { + content: "\f150"; } + +.fa-caret-square-down::before { + content: "\f150"; } + +.fa-file-circle-question::before { + content: "\e4ef"; } + +.fa-laptop-code::before { + content: "\f5fc"; } + +.fa-swatchbook::before { + content: "\f5c3"; } + +.fa-prescription-bottle::before { + content: "\f485"; } + +.fa-bars::before { + content: "\f0c9"; } + +.fa-navicon::before { + content: "\f0c9"; } + +.fa-people-group::before { + content: "\e533"; } + +.fa-hourglass-end::before { + content: "\f253"; } + +.fa-hourglass-3::before { + content: "\f253"; } + +.fa-heart-crack::before { + content: "\f7a9"; } + +.fa-heart-broken::before { + content: "\f7a9"; } + +.fa-square-up-right::before { + content: "\f360"; } + +.fa-external-link-square-alt::before { + content: "\f360"; } + +.fa-face-kiss-beam::before { + content: "\f597"; } + +.fa-kiss-beam::before { + content: "\f597"; } + +.fa-film::before { + content: "\f008"; } + +.fa-ruler-horizontal::before { + content: "\f547"; } + +.fa-people-robbery::before { + content: "\e536"; } + +.fa-lightbulb::before { + content: "\f0eb"; } + +.fa-caret-left::before { + content: "\f0d9"; } + +.fa-circle-exclamation::before { + content: "\f06a"; } + +.fa-exclamation-circle::before { + content: "\f06a"; } + +.fa-school-circle-xmark::before { + content: "\e56d"; } + +.fa-arrow-right-from-bracket::before { + content: "\f08b"; } + +.fa-sign-out::before { + content: "\f08b"; } + +.fa-circle-chevron-down::before { + content: "\f13a"; } + +.fa-chevron-circle-down::before { + content: "\f13a"; } + +.fa-unlock-keyhole::before { + content: "\f13e"; } + +.fa-unlock-alt::before { + content: "\f13e"; } + +.fa-cloud-showers-heavy::before { + content: "\f740"; } + +.fa-headphones-simple::before { + content: "\f58f"; } + +.fa-headphones-alt::before { + content: "\f58f"; } + +.fa-sitemap::before { + content: "\f0e8"; } + +.fa-circle-dollar-to-slot::before { + content: "\f4b9"; } + +.fa-donate::before { + content: "\f4b9"; } + +.fa-memory::before { + content: "\f538"; } + +.fa-road-spikes::before { + content: "\e568"; } + +.fa-fire-burner::before { + content: "\e4f1"; } + +.fa-flag::before { + content: "\f024"; } + +.fa-hanukiah::before { + content: "\f6e6"; } + +.fa-feather::before { + content: "\f52d"; } + +.fa-volume-low::before { + content: "\f027"; } + +.fa-volume-down::before { + content: "\f027"; } + +.fa-comment-slash::before { + content: "\f4b3"; } + +.fa-cloud-sun-rain::before { + content: "\f743"; } + +.fa-compress::before { + content: "\f066"; } + +.fa-wheat-awn::before { + content: "\e2cd"; } + +.fa-wheat-alt::before { + content: "\e2cd"; } + +.fa-ankh::before { + content: "\f644"; } + +.fa-hands-holding-child::before { + content: "\e4fa"; } + +.fa-asterisk::before { + content: "\2a"; } + +.fa-square-check::before { + content: "\f14a"; } + +.fa-check-square::before { + content: "\f14a"; } + +.fa-peseta-sign::before { + content: "\e221"; } + +.fa-heading::before { + content: "\f1dc"; } + +.fa-header::before { + content: "\f1dc"; } + +.fa-ghost::before { + content: "\f6e2"; } + +.fa-list::before { + content: "\f03a"; } + +.fa-list-squares::before { + content: "\f03a"; } + +.fa-square-phone-flip::before { + content: "\f87b"; } + +.fa-phone-square-alt::before { + content: "\f87b"; } + +.fa-cart-plus::before { + content: "\f217"; } + +.fa-gamepad::before { + content: "\f11b"; } + +.fa-circle-dot::before { + content: "\f192"; } + +.fa-dot-circle::before { + content: "\f192"; } + +.fa-face-dizzy::before { + content: "\f567"; } + +.fa-dizzy::before { + content: "\f567"; } + +.fa-egg::before { + content: "\f7fb"; } + +.fa-house-medical-circle-xmark::before { + content: "\e513"; } + +.fa-campground::before { + content: "\f6bb"; } + +.fa-folder-plus::before { + content: "\f65e"; } + +.fa-futbol::before { + content: "\f1e3"; } + +.fa-futbol-ball::before { + content: "\f1e3"; } + +.fa-soccer-ball::before { + content: "\f1e3"; } + +.fa-paintbrush::before { + content: "\f1fc"; } + +.fa-paint-brush::before { + content: "\f1fc"; } + +.fa-lock::before { + content: "\f023"; } + +.fa-gas-pump::before { + content: "\f52f"; } + +.fa-hot-tub-person::before { + content: "\f593"; } + +.fa-hot-tub::before { + content: "\f593"; } + +.fa-map-location::before { + content: "\f59f"; } + +.fa-map-marked::before { + content: "\f59f"; } + +.fa-house-flood-water::before { + content: "\e50e"; } + +.fa-tree::before { + content: "\f1bb"; } + +.fa-bridge-lock::before { + content: "\e4cc"; } + +.fa-sack-dollar::before { + content: "\f81d"; } + +.fa-pen-to-square::before { + content: "\f044"; } + +.fa-edit::before { + content: "\f044"; } + +.fa-car-side::before { + content: "\f5e4"; } + +.fa-share-nodes::before { + content: "\f1e0"; } + +.fa-share-alt::before { + content: "\f1e0"; } + +.fa-heart-circle-minus::before { + content: "\e4ff"; } + +.fa-hourglass-half::before { + content: "\f252"; } + +.fa-hourglass-2::before { + content: "\f252"; } + +.fa-microscope::before { + content: "\f610"; } + +.fa-sink::before { + content: "\e06d"; } + +.fa-bag-shopping::before { + content: "\f290"; } + +.fa-shopping-bag::before { + content: "\f290"; } + +.fa-arrow-down-z-a::before { + content: "\f881"; } + +.fa-sort-alpha-desc::before { + content: "\f881"; } + +.fa-sort-alpha-down-alt::before { + content: "\f881"; } + +.fa-mitten::before { + content: "\f7b5"; } + +.fa-person-rays::before { + content: "\e54d"; } + 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content: "\e509"; } + +.fa-angle-left::before { + content: "\f104"; } + +.fa-diagram-successor::before { + content: "\e47a"; } + +.fa-truck-arrow-right::before { + content: "\e58b"; } + +.fa-arrows-split-up-and-left::before { + content: "\e4bc"; } + +.fa-hand-fist::before { + content: "\f6de"; } + +.fa-fist-raised::before { + content: "\f6de"; } + +.fa-cloud-moon::before { + content: "\f6c3"; } + +.fa-briefcase::before { + content: "\f0b1"; } + +.fa-person-falling::before { + content: "\e546"; } + +.fa-image-portrait::before { + content: "\f3e0"; } + +.fa-portrait::before { + content: "\f3e0"; } + +.fa-user-tag::before { + content: "\f507"; } + +.fa-rug::before { + content: "\e569"; } + +.fa-earth-europe::before { + content: "\f7a2"; } + +.fa-globe-europe::before { + content: "\f7a2"; } + +.fa-cart-flatbed-suitcase::before { + content: "\f59d"; } + +.fa-luggage-cart::before { + content: "\f59d"; } + +.fa-rectangle-xmark::before { + content: "\f410"; } + +.fa-rectangle-times::before { + content: "\f410"; } + +.fa-times-rectangle::before { + content: "\f410"; } + +.fa-window-close::before { + content: "\f410"; } + +.fa-baht-sign::before { + content: "\e0ac"; } + +.fa-book-open::before { + content: "\f518"; } + +.fa-book-journal-whills::before { + content: "\f66a"; } + +.fa-journal-whills::before { + content: "\f66a"; } + +.fa-handcuffs::before { + content: "\e4f8"; } + +.fa-triangle-exclamation::before { + content: "\f071"; } + +.fa-exclamation-triangle::before { + content: "\f071"; } + +.fa-warning::before { + content: "\f071"; } + +.fa-database::before { + content: "\f1c0"; } + +.fa-share::before { + content: "\f064"; } + +.fa-arrow-turn-right::before { + content: "\f064"; } + +.fa-mail-forward::before { + content: "\f064"; } + +.fa-bottle-droplet::before { + content: "\e4c4"; } + +.fa-mask-face::before { + content: "\e1d7"; } + +.fa-hill-rockslide::before { + content: "\e508"; } + +.fa-right-left::before { + content: "\f362"; } + +.fa-exchange-alt::before { + content: "\f362"; } + +.fa-paper-plane::before { + content: "\f1d8"; } + +.fa-road-circle-exclamation::before { + content: "\e565"; } + +.fa-dungeon::before { + content: "\f6d9"; } + +.fa-align-right::before { + content: "\f038"; } + +.fa-money-bill-1-wave::before { + content: "\f53b"; } + +.fa-money-bill-wave-alt::before { + content: "\f53b"; } + +.fa-life-ring::before { + content: "\f1cd"; } + +.fa-hands::before { + content: "\f2a7"; } + +.fa-sign-language::before { + content: "\f2a7"; } + +.fa-signing::before { + content: "\f2a7"; } + +.fa-calendar-day::before { + content: "\f783"; } + +.fa-water-ladder::before { + content: "\f5c5"; } + +.fa-ladder-water::before { + content: "\f5c5"; } + +.fa-swimming-pool::before { + content: "\f5c5"; } + +.fa-arrows-up-down::before { + content: "\f07d"; } + +.fa-arrows-v::before { + content: "\f07d"; } + +.fa-face-grimace::before { + content: "\f57f"; } + +.fa-grimace::before { + content: "\f57f"; } + +.fa-wheelchair-move::before { + content: 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content: "\e5b4"; } + +.fa-user-nurse::before { + content: "\f82f"; } + +.fa-syringe::before { + content: "\f48e"; } + +.fa-cloud-sun::before { + content: "\f6c4"; } + +.fa-stopwatch-20::before { + content: "\e06f"; } + +.fa-square-full::before { + content: "\f45c"; } + +.fa-magnet::before { + content: "\f076"; } + +.fa-jar::before { + content: "\e516"; } + +.fa-note-sticky::before { + content: "\f249"; } + +.fa-sticky-note::before { + content: "\f249"; } + +.fa-bug-slash::before { + content: "\e490"; } + +.fa-arrow-up-from-water-pump::before { + content: "\e4b6"; } + +.fa-bone::before { + content: "\f5d7"; } + +.fa-user-injured::before { + content: "\f728"; } + +.fa-face-sad-tear::before { + content: "\f5b4"; } + +.fa-sad-tear::before { + content: "\f5b4"; } + +.fa-plane::before { + content: "\f072"; } + +.fa-tent-arrows-down::before { + content: "\e581"; } + +.fa-exclamation::before { + content: "\21"; } + +.fa-arrows-spin::before { + content: "\e4bb"; } + +.fa-print::before { + content: "\f02f"; } + +.fa-turkish-lira-sign::before { + content: "\e2bb"; } + +.fa-try::before { + content: "\e2bb"; } + +.fa-turkish-lira::before { + content: "\e2bb"; } + +.fa-dollar-sign::before { + content: "\24"; } + +.fa-dollar::before { + content: "\24"; } + +.fa-usd::before { + content: "\24"; } + +.fa-x::before { + content: "\58"; } + +.fa-magnifying-glass-dollar::before { + content: "\f688"; } + +.fa-search-dollar::before { + content: "\f688"; } + +.fa-users-gear::before { + content: "\f509"; } + +.fa-users-cog::before { + content: "\f509"; } + +.fa-person-military-pointing::before { + content: "\e54a"; } + +.fa-building-columns::before { + content: "\f19c"; } + +.fa-bank::before { + content: "\f19c"; } + +.fa-institution::before { + content: "\f19c"; } + +.fa-museum::before { + content: "\f19c"; } + +.fa-university::before { + content: "\f19c"; } + +.fa-umbrella::before { + content: "\f0e9"; } + +.fa-trowel::before { + content: "\e589"; } + +.fa-d::before { + content: 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"\e53e"; } + +.fa-turn-up::before { + content: "\f3bf"; } + +.fa-level-up-alt::before { + content: "\f3bf"; } + +.sr-only, +.fa-sr-only { + position: absolute; + width: 1px; + height: 1px; + padding: 0; + margin: -1px; + overflow: hidden; + clip: rect(0, 0, 0, 0); + white-space: nowrap; + border-width: 0; } + +.sr-only-focusable:not(:focus), +.fa-sr-only-focusable:not(:focus) { + position: absolute; + width: 1px; + height: 1px; + padding: 0; + margin: -1px; + overflow: hidden; + clip: rect(0, 0, 0, 0); + white-space: nowrap; + border-width: 0; } +:root, :host { + --fa-style-family-brands: 'Font Awesome 6 Brands'; + --fa-font-brands: normal 400 1em/1 'Font Awesome 6 Brands'; } + +@font-face { + font-family: 'Font Awesome 6 Brands'; + font-style: normal; + font-weight: 400; + font-display: block; + src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); } + +.fab, +.fa-brands { + font-weight: 400; } + +.fa-monero:before { + content: "\f3d0"; } + +.fa-hooli:before { + content: "\f427"; } + +.fa-yelp:before { + content: "\f1e9"; } + +.fa-cc-visa:before { + content: "\f1f0"; } + +.fa-lastfm:before { + content: "\f202"; } + +.fa-shopware:before { + content: "\f5b5"; } + +.fa-creative-commons-nc:before { + content: "\f4e8"; } + +.fa-aws:before { + content: "\f375"; } + +.fa-redhat:before { + content: "\f7bc"; } + +.fa-yoast:before { + content: "\f2b1"; } + +.fa-cloudflare:before { + content: "\e07d"; } + +.fa-ups:before { + content: "\f7e0"; } + +.fa-wpexplorer:before { + content: "\f2de"; } + +.fa-dyalog:before { + content: "\f399"; } + +.fa-bity:before { + content: "\f37a"; } + +.fa-stackpath:before { + content: "\f842"; } + +.fa-buysellads:before { + content: "\f20d"; } + +.fa-first-order:before { + content: "\f2b0"; } + +.fa-modx:before { + content: "\f285"; } + +.fa-guilded:before { + content: "\e07e"; } + +.fa-vnv:before { + content: "\f40b"; } + +.fa-square-js:before { + content: "\f3b9"; } + 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content: "\f7d3"; } + +.fa-google-plus:before { + content: "\f2b3"; } + +.fa-diaspora:before { + content: "\f791"; } + +.fa-foursquare:before { + content: "\f180"; } + +.fa-stack-overflow:before { + content: "\f16c"; } + +.fa-github-alt:before { + content: "\f113"; } + +.fa-phoenix-squadron:before { + content: "\f511"; } + +.fa-pagelines:before { + content: "\f18c"; } + +.fa-algolia:before { + content: "\f36c"; } + +.fa-red-river:before { + content: "\f3e3"; } + +.fa-creative-commons-sa:before { + content: "\f4ef"; } + +.fa-safari:before { + content: "\f267"; } + +.fa-google:before { + content: "\f1a0"; } + +.fa-square-font-awesome-stroke:before { + content: "\f35c"; } + +.fa-font-awesome-alt:before { + content: "\f35c"; } + +.fa-atlassian:before { + content: "\f77b"; } + +.fa-linkedin-in:before { + content: "\f0e1"; } + +.fa-digital-ocean:before { + content: "\f391"; } + +.fa-nimblr:before { + content: "\f5a8"; } + +.fa-chromecast:before { + content: "\f838"; } + +.fa-evernote:before 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+.fa.fa-external-link:before { + content: "\f35d"; } + +.fa.fa-sign-in:before { + content: "\f2f6"; } + +.fa.fa-github-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-github-square:before { + content: "\f092"; } + +.fa.fa-lemon-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-lemon-o:before { + content: "\f094"; } + +.fa.fa-square-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-square-o:before { + content: "\f0c8"; } + +.fa.fa-bookmark-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-bookmark-o:before { + content: "\f02e"; } + +.fa.fa-twitter { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-facebook { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-facebook:before { + content: "\f39e"; } + +.fa.fa-facebook-f { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-facebook-f:before { + content: "\f39e"; } + +.fa.fa-github { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-credit-card { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-feed:before { + content: "\f09e"; } + +.fa.fa-hdd-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hdd-o:before { + content: "\f0a0"; } + +.fa.fa-hand-o-right { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-o-right:before { + content: "\f0a4"; } + +.fa.fa-hand-o-left { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-o-left:before { + content: "\f0a5"; } + +.fa.fa-hand-o-up { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-o-up:before { + content: "\f0a6"; } + +.fa.fa-hand-o-down { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-o-down:before { + content: "\f0a7"; } + +.fa.fa-globe:before { + content: "\f57d"; } + +.fa.fa-tasks:before { + content: "\f828"; } + +.fa.fa-arrows-alt:before { + content: "\f31e"; } + +.fa.fa-group:before { + content: "\f0c0"; } + +.fa.fa-chain:before { + content: "\f0c1"; } + +.fa.fa-cut:before { + content: "\f0c4"; } + +.fa.fa-files-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-files-o:before { + content: "\f0c5"; } + +.fa.fa-floppy-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-floppy-o:before { + content: "\f0c7"; } + +.fa.fa-save { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-save:before { + content: "\f0c7"; } + +.fa.fa-navicon:before { + content: "\f0c9"; } + +.fa.fa-reorder:before { + content: "\f0c9"; } + +.fa.fa-magic:before { + content: "\e2ca"; } + +.fa.fa-pinterest { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-pinterest-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-pinterest-square:before { + content: "\f0d3"; } + +.fa.fa-google-plus-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-google-plus-square:before { + content: "\f0d4"; } + +.fa.fa-google-plus { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-google-plus:before { + content: "\f0d5"; } + +.fa.fa-money:before { + content: "\f3d1"; } + +.fa.fa-unsorted:before { + content: "\f0dc"; } + +.fa.fa-sort-desc:before { + content: "\f0dd"; } + +.fa.fa-sort-asc:before { + content: "\f0de"; } + +.fa.fa-linkedin { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-linkedin:before { + content: "\f0e1"; } + +.fa.fa-rotate-left:before { + content: "\f0e2"; } + +.fa.fa-legal:before { + content: "\f0e3"; } + +.fa.fa-tachometer:before { + content: "\f625"; } + +.fa.fa-dashboard:before { + content: "\f625"; } + +.fa.fa-comment-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-comment-o:before { + content: "\f075"; } + +.fa.fa-comments-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-comments-o:before { + content: "\f086"; } + +.fa.fa-flash:before { + content: "\f0e7"; } + +.fa.fa-clipboard:before { + content: "\f0ea"; } + +.fa.fa-lightbulb-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-lightbulb-o:before { + content: "\f0eb"; } + +.fa.fa-exchange:before { + content: "\f362"; } + +.fa.fa-cloud-download:before { + content: "\f0ed"; } + +.fa.fa-cloud-upload:before { + content: "\f0ee"; } + +.fa.fa-bell-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-bell-o:before { + content: "\f0f3"; } + +.fa.fa-cutlery:before { + content: "\f2e7"; } + +.fa.fa-file-text-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-text-o:before { + content: "\f15c"; } + +.fa.fa-building-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-building-o:before { + content: "\f1ad"; } + +.fa.fa-hospital-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hospital-o:before { + content: "\f0f8"; } + +.fa.fa-tablet:before { + content: "\f3fa"; } + +.fa.fa-mobile:before { + content: "\f3cd"; } + +.fa.fa-mobile-phone:before { + content: "\f3cd"; } + +.fa.fa-circle-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-circle-o:before { + content: "\f111"; } + +.fa.fa-mail-reply:before { + content: "\f3e5"; } + +.fa.fa-github-alt { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-folder-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-folder-o:before { + content: "\f07b"; } + +.fa.fa-folder-open-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-folder-open-o:before { + content: "\f07c"; } + +.fa.fa-smile-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-smile-o:before { + content: "\f118"; } + +.fa.fa-frown-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-frown-o:before { + content: "\f119"; } + +.fa.fa-meh-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-meh-o:before { + content: "\f11a"; } + +.fa.fa-keyboard-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-keyboard-o:before { + content: "\f11c"; } + +.fa.fa-flag-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-flag-o:before { + content: "\f024"; } + +.fa.fa-mail-reply-all:before { + content: "\f122"; } + +.fa.fa-star-half-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-star-half-o:before { + content: "\f5c0"; } + +.fa.fa-star-half-empty { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-star-half-empty:before { + content: "\f5c0"; } + +.fa.fa-star-half-full { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-star-half-full:before { + content: "\f5c0"; } + +.fa.fa-code-fork:before { + content: "\f126"; } + +.fa.fa-chain-broken:before { + content: "\f127"; } + +.fa.fa-unlink:before { + content: "\f127"; } + +.fa.fa-calendar-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-calendar-o:before { + content: "\f133"; } + +.fa.fa-maxcdn { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-html5 { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-css3 { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-unlock-alt:before { + content: "\f09c"; } + +.fa.fa-minus-square-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-minus-square-o:before { + content: "\f146"; } + +.fa.fa-level-up:before { + content: "\f3bf"; } + +.fa.fa-level-down:before { + content: "\f3be"; } + +.fa.fa-pencil-square:before { + content: "\f14b"; } + +.fa.fa-external-link-square:before { + content: "\f360"; } + +.fa.fa-compass { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-caret-square-o-down { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-caret-square-o-down:before { + content: "\f150"; } + +.fa.fa-toggle-down { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-toggle-down:before { + content: "\f150"; } + +.fa.fa-caret-square-o-up { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-caret-square-o-up:before { + content: "\f151"; } + +.fa.fa-toggle-up { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-toggle-up:before { + content: "\f151"; } + +.fa.fa-caret-square-o-right { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-caret-square-o-right:before { + content: "\f152"; } + +.fa.fa-toggle-right { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-toggle-right:before { + content: "\f152"; } + +.fa.fa-eur:before { + content: "\f153"; } + +.fa.fa-euro:before { + content: "\f153"; } + +.fa.fa-gbp:before { + content: "\f154"; } + +.fa.fa-usd:before { + content: "\24"; } + +.fa.fa-dollar:before { + content: "\24"; } + +.fa.fa-inr:before { + content: "\e1bc"; } + +.fa.fa-rupee:before { + content: "\e1bc"; } + +.fa.fa-jpy:before { + content: "\f157"; } + +.fa.fa-cny:before { + content: "\f157"; } + +.fa.fa-rmb:before { + content: "\f157"; } + +.fa.fa-yen:before { + content: "\f157"; } + +.fa.fa-rub:before { + content: "\f158"; } + +.fa.fa-ruble:before { + content: "\f158"; } + +.fa.fa-rouble:before { + content: "\f158"; } + +.fa.fa-krw:before { + content: "\f159"; } + +.fa.fa-won:before { + content: "\f159"; } + +.fa.fa-btc { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-bitcoin { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-bitcoin:before { + content: "\f15a"; } + +.fa.fa-file-text:before { + content: "\f15c"; } + +.fa.fa-sort-alpha-asc:before { + content: "\f15d"; } + +.fa.fa-sort-alpha-desc:before { + content: "\f881"; } + +.fa.fa-sort-amount-asc:before { + content: "\f884"; } + +.fa.fa-sort-amount-desc:before { + content: "\f160"; } + +.fa.fa-sort-numeric-asc:before { + content: "\f162"; } + +.fa.fa-sort-numeric-desc:before { + content: "\f886"; } + +.fa.fa-youtube-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-youtube-square:before { + content: "\f431"; } + +.fa.fa-youtube { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-xing { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-xing-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-xing-square:before { + content: "\f169"; } + +.fa.fa-youtube-play { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-youtube-play:before { + content: "\f167"; } + +.fa.fa-dropbox { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-stack-overflow { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-instagram { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-flickr { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-adn { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-bitbucket { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-bitbucket-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-bitbucket-square:before { + content: "\f171"; } + +.fa.fa-tumblr { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-tumblr-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-tumblr-square:before { + content: "\f174"; } + +.fa.fa-long-arrow-down:before { + content: "\f309"; } + +.fa.fa-long-arrow-up:before { + content: "\f30c"; } + +.fa.fa-long-arrow-left:before { + content: "\f30a"; } + +.fa.fa-long-arrow-right:before { + content: "\f30b"; } + +.fa.fa-apple { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-windows { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-android { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-linux { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-dribbble { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-skype { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-foursquare { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-trello { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-gratipay { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-gittip { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-gittip:before { + content: "\f184"; } + +.fa.fa-sun-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-sun-o:before { + content: "\f185"; } + +.fa.fa-moon-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-moon-o:before { + content: "\f186"; } + +.fa.fa-vk { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-weibo { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-renren { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-pagelines { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-stack-exchange { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-arrow-circle-o-right { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-arrow-circle-o-right:before { + content: "\f35a"; } + +.fa.fa-arrow-circle-o-left { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-arrow-circle-o-left:before { + content: "\f359"; } + +.fa.fa-caret-square-o-left { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-caret-square-o-left:before { + content: "\f191"; } + +.fa.fa-toggle-left { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-toggle-left:before { + content: "\f191"; } + +.fa.fa-dot-circle-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-dot-circle-o:before { + content: "\f192"; } + +.fa.fa-vimeo-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-vimeo-square:before { + content: "\f194"; } + +.fa.fa-try:before { + content: "\e2bb"; } + +.fa.fa-turkish-lira:before { + content: "\e2bb"; } + +.fa.fa-plus-square-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-plus-square-o:before { + content: "\f0fe"; } + +.fa.fa-slack { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-wordpress { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-openid { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-institution:before { + content: "\f19c"; } + +.fa.fa-bank:before { + content: "\f19c"; } + +.fa.fa-mortar-board:before { + content: "\f19d"; } + +.fa.fa-yahoo { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-google { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-reddit { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-reddit-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-reddit-square:before { + content: "\f1a2"; } + +.fa.fa-stumbleupon-circle { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-stumbleupon { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-delicious { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-digg { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-pied-piper-pp { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-pied-piper-alt { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-drupal { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-joomla { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-behance { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-behance-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-behance-square:before { + content: "\f1b5"; } + +.fa.fa-steam { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-steam-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-steam-square:before { + content: "\f1b7"; } + +.fa.fa-automobile:before { + content: "\f1b9"; } + +.fa.fa-cab:before { + content: "\f1ba"; } + +.fa.fa-spotify { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-deviantart { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-soundcloud { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-file-pdf-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-pdf-o:before { + content: "\f1c1"; } + +.fa.fa-file-word-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-word-o:before { + content: "\f1c2"; } + +.fa.fa-file-excel-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-excel-o:before { + content: "\f1c3"; } + +.fa.fa-file-powerpoint-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-powerpoint-o:before { + content: "\f1c4"; } + +.fa.fa-file-image-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-image-o:before { + content: "\f1c5"; } + +.fa.fa-file-photo-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-photo-o:before { + content: "\f1c5"; } + +.fa.fa-file-picture-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-picture-o:before { + content: "\f1c5"; } + +.fa.fa-file-archive-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-archive-o:before { + content: "\f1c6"; } + +.fa.fa-file-zip-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-zip-o:before { + content: "\f1c6"; } + +.fa.fa-file-audio-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-audio-o:before { + content: "\f1c7"; } + +.fa.fa-file-sound-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-sound-o:before { + content: "\f1c7"; } + +.fa.fa-file-video-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-video-o:before { + content: "\f1c8"; } + +.fa.fa-file-movie-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-movie-o:before { + content: "\f1c8"; } + +.fa.fa-file-code-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-file-code-o:before { + content: "\f1c9"; } + +.fa.fa-vine { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-codepen { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-jsfiddle { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-life-bouy:before { + content: "\f1cd"; } + +.fa.fa-life-buoy:before { + content: "\f1cd"; } + +.fa.fa-life-saver:before { + content: "\f1cd"; } + +.fa.fa-support:before { + content: "\f1cd"; } + +.fa.fa-circle-o-notch:before { + content: "\f1ce"; } + +.fa.fa-rebel { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-ra { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-ra:before { + content: "\f1d0"; } + +.fa.fa-resistance { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-resistance:before { + content: "\f1d0"; } + +.fa.fa-empire { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-ge { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-ge:before { + content: "\f1d1"; } + +.fa.fa-git-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-git-square:before { + content: "\f1d2"; } + +.fa.fa-git { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-hacker-news { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-y-combinator-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-y-combinator-square:before { + content: "\f1d4"; } + +.fa.fa-yc-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-yc-square:before { + content: "\f1d4"; } + +.fa.fa-tencent-weibo { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-qq { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-weixin { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-wechat { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-wechat:before { + content: "\f1d7"; } + +.fa.fa-send:before { + content: "\f1d8"; } + +.fa.fa-paper-plane-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-paper-plane-o:before { + content: "\f1d8"; } + +.fa.fa-send-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-send-o:before { + content: "\f1d8"; } + +.fa.fa-circle-thin { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-circle-thin:before { + content: "\f111"; } + +.fa.fa-header:before { + content: "\f1dc"; } + +.fa.fa-futbol-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-futbol-o:before { + content: "\f1e3"; } + +.fa.fa-soccer-ball-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-soccer-ball-o:before { + content: "\f1e3"; } + +.fa.fa-slideshare { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-twitch { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-yelp { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-newspaper-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-newspaper-o:before { + content: "\f1ea"; } + +.fa.fa-paypal { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-google-wallet { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-cc-visa { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-cc-mastercard { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-cc-discover { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-cc-amex { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-cc-paypal { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-cc-stripe { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-bell-slash-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-bell-slash-o:before { + content: "\f1f6"; } + +.fa.fa-trash:before { + content: "\f2ed"; } + +.fa.fa-copyright { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-eyedropper:before { + content: "\f1fb"; } + +.fa.fa-area-chart:before { + content: "\f1fe"; } + +.fa.fa-pie-chart:before { + content: "\f200"; } + +.fa.fa-line-chart:before { + content: "\f201"; } + +.fa.fa-lastfm { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-lastfm-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-lastfm-square:before { + content: "\f203"; } + +.fa.fa-ioxhost { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-angellist { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-cc { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-cc:before { + content: "\f20a"; } + +.fa.fa-ils:before { + content: "\f20b"; } + +.fa.fa-shekel:before { + content: "\f20b"; } + +.fa.fa-sheqel:before { + content: "\f20b"; } + +.fa.fa-buysellads { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-connectdevelop { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-dashcube { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-forumbee { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-leanpub { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-sellsy { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-shirtsinbulk { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-simplybuilt { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-skyatlas { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-diamond { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-diamond:before { + content: "\f3a5"; } + +.fa.fa-transgender:before { + content: "\f224"; } + +.fa.fa-intersex:before { + content: "\f224"; } + +.fa.fa-transgender-alt:before { + content: "\f225"; } + +.fa.fa-facebook-official { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-facebook-official:before { + content: "\f09a"; } + +.fa.fa-pinterest-p { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-whatsapp { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-hotel:before { + content: "\f236"; } + +.fa.fa-viacoin { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-medium { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-y-combinator { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-yc { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-yc:before { + content: "\f23b"; } + +.fa.fa-optin-monster { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-opencart { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-expeditedssl { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-battery-4:before { + content: "\f240"; } + +.fa.fa-battery:before { + content: "\f240"; } + +.fa.fa-battery-3:before { + content: "\f241"; } + +.fa.fa-battery-2:before { + content: "\f242"; } + +.fa.fa-battery-1:before { + content: "\f243"; } + +.fa.fa-battery-0:before { + content: "\f244"; } + +.fa.fa-object-group { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-object-ungroup { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-sticky-note-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-sticky-note-o:before { + content: "\f249"; } + +.fa.fa-cc-jcb { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-cc-diners-club { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-clone { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hourglass-o:before { + content: "\f254"; } + +.fa.fa-hourglass-1:before { + content: "\f251"; } + +.fa.fa-hourglass-2:before { + content: "\f252"; } + +.fa.fa-hourglass-3:before { + content: "\f253"; } + +.fa.fa-hand-rock-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-rock-o:before { + content: "\f255"; } + +.fa.fa-hand-grab-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-grab-o:before { + content: "\f255"; } + +.fa.fa-hand-paper-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-paper-o:before { + content: "\f256"; } + +.fa.fa-hand-stop-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-stop-o:before { + content: "\f256"; } + +.fa.fa-hand-scissors-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-scissors-o:before { + content: "\f257"; } + +.fa.fa-hand-lizard-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-lizard-o:before { + content: "\f258"; } + +.fa.fa-hand-spock-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-spock-o:before { + content: "\f259"; } + +.fa.fa-hand-pointer-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-pointer-o:before { + content: "\f25a"; } + +.fa.fa-hand-peace-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-hand-peace-o:before { + content: "\f25b"; } + +.fa.fa-registered { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-creative-commons { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-gg { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-gg-circle { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-odnoklassniki { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-odnoklassniki-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-odnoklassniki-square:before { + content: "\f264"; } + +.fa.fa-get-pocket { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-wikipedia-w { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-safari { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-chrome { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-firefox { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-opera { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-internet-explorer { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-television:before { + content: "\f26c"; } + +.fa.fa-contao { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-500px { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-amazon { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-calendar-plus-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-calendar-plus-o:before { + content: "\f271"; } + +.fa.fa-calendar-minus-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-calendar-minus-o:before { + content: "\f272"; } + +.fa.fa-calendar-times-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-calendar-times-o:before { + content: "\f273"; } + +.fa.fa-calendar-check-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-calendar-check-o:before { + content: "\f274"; } + +.fa.fa-map-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-map-o:before { + content: "\f279"; } + +.fa.fa-commenting:before { + content: "\f4ad"; } + +.fa.fa-commenting-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-commenting-o:before { + content: "\f4ad"; } + +.fa.fa-houzz { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-vimeo { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-vimeo:before { + content: "\f27d"; } + +.fa.fa-black-tie { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-fonticons { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-reddit-alien { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-edge { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-credit-card-alt:before { + content: "\f09d"; } + +.fa.fa-codiepie { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-modx { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-fort-awesome { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-usb { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-product-hunt { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-mixcloud { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-scribd { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-pause-circle-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-pause-circle-o:before { + content: "\f28b"; } + +.fa.fa-stop-circle-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-stop-circle-o:before { + content: "\f28d"; } + +.fa.fa-bluetooth { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-bluetooth-b { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-gitlab { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-wpbeginner { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-wpforms { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-envira { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-wheelchair-alt { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-wheelchair-alt:before { + content: "\f368"; } + +.fa.fa-question-circle-o { + font-family: 'Font Awesome 6 Free'; + font-weight: 400; } + +.fa.fa-question-circle-o:before { + content: "\f059"; } + +.fa.fa-volume-control-phone:before { + content: "\f2a0"; } + +.fa.fa-asl-interpreting:before { + content: "\f2a3"; } + +.fa.fa-deafness:before { + content: "\f2a4"; } + +.fa.fa-hard-of-hearing:before { + content: "\f2a4"; } + +.fa.fa-glide { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-glide-g { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-signing:before { + content: "\f2a7"; } + +.fa.fa-viadeo { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-viadeo-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-viadeo-square:before { + content: "\f2aa"; } + +.fa.fa-snapchat { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-snapchat-ghost { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-snapchat-ghost:before { + content: "\f2ab"; } + +.fa.fa-snapchat-square { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-snapchat-square:before { + content: "\f2ad"; } + +.fa.fa-pied-piper { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-first-order { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; } + +.fa.fa-yoast { + font-family: 'Font Awesome 6 Brands'; + font-weight: 400; 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Hide your header until you need it + * Copyright (c) 2017 Nick Williams - http://wicky.nillia.ms/headroom.js + * License: MIT + */ + +!function(a){a&&(a.fn.headroom=function(b){return this.each(function(){var c=a(this),d=c.data("headroom"),e="object"==typeof b&&b;e=a.extend(!0,{},Headroom.options,e),d||(d=new Headroom(this,e),d.init(),c.data("headroom",d)),"string"==typeof b&&(d[b](),"destroy"===b&&c.removeData("headroom"))})},a("[data-headroom]").each(function(){var b=a(this);b.headroom(b.data())}))}(window.Zepto||window.jQuery); \ No newline at end of file diff --git a/deps/jquery-3.6.0/jquery-3.6.0.js b/deps/jquery-3.6.0/jquery-3.6.0.js new file mode 100644 index 00000000..fc6c299b --- /dev/null +++ b/deps/jquery-3.6.0/jquery-3.6.0.js @@ -0,0 +1,10881 @@ +/*! + * jQuery JavaScript Library v3.6.0 + * https://jquery.com/ + * + * Includes Sizzle.js + * https://sizzlejs.com/ + * + * Copyright OpenJS Foundation and other contributors + * Released under the MIT license + * https://jquery.org/license + * + * Date: 2021-03-02T17:08Z + */ +( function( global, factory ) { + + "use strict"; + + if ( typeof module === "object" && typeof module.exports === "object" ) { + + // For CommonJS and CommonJS-like environments where a proper `window` + // is present, execute the factory and get jQuery. + // For environments that do not have a `window` with a `document` + // (such as Node.js), expose a factory as module.exports. + // This accentuates the need for the creation of a real `window`. + // e.g. var jQuery = require("jquery")(window); + // See ticket #14549 for more info. + module.exports = global.document ? + factory( global, true ) : + function( w ) { + if ( !w.document ) { + throw new Error( "jQuery requires a window with a document" ); + } + return factory( w ); + }; + } else { + factory( global ); + } + +// Pass this if window is not defined yet +} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) { + +// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1 +// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode +// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common +// enough that all such attempts are guarded in a try block. +"use strict"; + +var arr = []; + +var getProto = Object.getPrototypeOf; + +var slice = arr.slice; + +var flat = arr.flat ? function( array ) { + return arr.flat.call( array ); +} : function( array ) { + return arr.concat.apply( [], array ); +}; + + +var push = arr.push; + +var indexOf = arr.indexOf; + +var class2type = {}; + +var toString = class2type.toString; + +var hasOwn = class2type.hasOwnProperty; + +var fnToString = hasOwn.toString; + +var ObjectFunctionString = fnToString.call( Object ); + +var support = {}; + +var isFunction = function isFunction( obj ) { + + // Support: Chrome <=57, Firefox <=52 + // In some browsers, typeof returns "function" for HTML elements + // (i.e., `typeof document.createElement( "object" ) === "function"`). + // We don't want to classify *any* DOM node as a function. + // Support: QtWeb <=3.8.5, WebKit <=534.34, wkhtmltopdf tool <=0.12.5 + // Plus for old WebKit, typeof returns "function" for HTML collections + // (e.g., `typeof document.getElementsByTagName("div") === "function"`). (gh-4756) + return typeof obj === "function" && typeof obj.nodeType !== "number" && + typeof obj.item !== "function"; + }; + + +var isWindow = function isWindow( obj ) { + return obj != null && obj === obj.window; + }; + + +var document = window.document; + + + + var preservedScriptAttributes = { + type: true, + src: true, + nonce: true, + noModule: true + }; + + function DOMEval( code, node, doc ) { + doc = doc || document; + + var i, val, + script = doc.createElement( "script" ); + + script.text = code; + if ( node ) { + for ( i in preservedScriptAttributes ) { + + // Support: Firefox 64+, Edge 18+ + // Some browsers don't support the "nonce" property on scripts. + // On the other hand, just using `getAttribute` is not enough as + // the `nonce` attribute is reset to an empty string whenever it + // becomes browsing-context connected. + // See https://github.com/whatwg/html/issues/2369 + // See https://html.spec.whatwg.org/#nonce-attributes + // The `node.getAttribute` check was added for the sake of + // `jQuery.globalEval` so that it can fake a nonce-containing node + // via an object. + val = node[ i ] || node.getAttribute && node.getAttribute( i ); + if ( val ) { + script.setAttribute( i, val ); + } + } + } + doc.head.appendChild( script ).parentNode.removeChild( script ); + } + + +function toType( obj ) { + if ( obj == null ) { + return obj + ""; + } + + // Support: Android <=2.3 only (functionish RegExp) + return typeof obj === "object" || typeof obj === "function" ? + class2type[ toString.call( obj ) ] || "object" : + typeof obj; +} +/* global Symbol */ +// Defining this global in .eslintrc.json would create a danger of using the global +// unguarded in another place, it seems safer to define global only for this module + + + +var + version = "3.6.0", + + // Define a local copy of jQuery + jQuery = function( selector, context ) { + + // The jQuery object is actually just the init constructor 'enhanced' + // Need init if jQuery is called (just allow error to be thrown if not included) + return new jQuery.fn.init( selector, context ); + }; + +jQuery.fn = jQuery.prototype = { + + // The current version of jQuery being used + jquery: version, + + constructor: jQuery, + + // The default length of a jQuery object is 0 + length: 0, + + toArray: function() { + return slice.call( this ); + }, + + // Get the Nth element in the matched element set OR + // Get the whole matched element set as a clean array + get: function( num ) { + + // Return all the elements in a clean array + if ( num == null ) { + return slice.call( this ); + } + + // Return just the one element from the set + return num < 0 ? this[ num + this.length ] : this[ num ]; + }, + + // Take an array of elements and push it onto the stack + // (returning the new matched element set) + pushStack: function( elems ) { + + // Build a new jQuery matched element set + var ret = jQuery.merge( this.constructor(), elems ); + + // Add the old object onto the stack (as a reference) + ret.prevObject = this; + + // Return the newly-formed element set + return ret; + }, + + // Execute a callback for every element in the matched set. + each: function( callback ) { + return jQuery.each( this, callback ); + }, + + map: function( callback ) { + return this.pushStack( jQuery.map( this, function( elem, i ) { + return callback.call( elem, i, elem ); + } ) ); + }, + + slice: function() { + return this.pushStack( slice.apply( this, arguments ) ); + }, + + first: function() { + return this.eq( 0 ); + }, + + last: function() { + return this.eq( -1 ); + }, + + even: function() { + return this.pushStack( jQuery.grep( this, function( _elem, i ) { + return ( i + 1 ) % 2; + } ) ); + }, + + odd: function() { + return this.pushStack( jQuery.grep( this, function( _elem, i ) { + return i % 2; + } ) ); + }, + + eq: function( i ) { + var len = this.length, + j = +i + ( i < 0 ? len : 0 ); + return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] ); + }, + + end: function() { + return this.prevObject || this.constructor(); + }, + + // For internal use only. + // Behaves like an Array's method, not like a jQuery method. + push: push, + sort: arr.sort, + splice: arr.splice +}; + +jQuery.extend = jQuery.fn.extend = function() { + var options, name, src, copy, copyIsArray, clone, + target = arguments[ 0 ] || {}, + i = 1, + length = arguments.length, + deep = false; + + // Handle a deep copy situation + if ( typeof target === "boolean" ) { + deep = target; + + // Skip the boolean and the target + target = arguments[ i ] || {}; + i++; + } + + // Handle case when target is a string or something (possible in deep copy) + if ( typeof target !== "object" && !isFunction( target ) ) { + target = {}; + } + + // Extend jQuery itself if only one argument is passed + if ( i === length ) { + target = this; + i--; + } + + for ( ; i < length; i++ ) { + + // Only deal with non-null/undefined values + if ( ( options = arguments[ i ] ) != null ) { + + // Extend the base object + for ( name in options ) { + copy = options[ name ]; + + // Prevent Object.prototype pollution + // Prevent never-ending loop + if ( name === "__proto__" || target === copy ) { + continue; + } + + // Recurse if we're merging plain objects or arrays + if ( deep && copy && ( jQuery.isPlainObject( copy ) || + ( copyIsArray = Array.isArray( copy ) ) ) ) { + src = target[ name ]; + + // Ensure proper type for the source value + if ( copyIsArray && !Array.isArray( src ) ) { + clone = []; + } else if ( !copyIsArray && !jQuery.isPlainObject( src ) ) { + clone = {}; + } else { + clone = src; + } + copyIsArray = false; + + // Never move original objects, clone them + target[ name ] = jQuery.extend( deep, clone, copy ); + + // Don't bring in undefined values + } else if ( copy !== undefined ) { + target[ name ] = copy; + } + } + } + } + + // Return the modified object + return target; +}; + +jQuery.extend( { + + // Unique for each copy of jQuery on the page + expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), + + // Assume jQuery is ready without the ready module + isReady: true, + + error: function( msg ) { + throw new Error( msg ); + }, + + noop: function() {}, + + isPlainObject: function( obj ) { + var proto, Ctor; + + // Detect obvious negatives + // Use toString instead of jQuery.type to catch host objects + if ( !obj || toString.call( obj ) !== "[object Object]" ) { + return false; + } + + proto = getProto( obj ); + + // Objects with no prototype (e.g., `Object.create( null )`) are plain + if ( !proto ) { + return true; + } + + // Objects with prototype are plain iff they were constructed by a global Object function + Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor; + return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString; + }, + + isEmptyObject: function( obj ) { + var name; + + for ( name in obj ) { + return false; + } + return true; + }, + + // Evaluates a script in a provided context; falls back to the global one + // if not specified. + globalEval: function( code, options, doc ) { + DOMEval( code, { nonce: options && options.nonce }, doc ); + }, + + each: function( obj, callback ) { + var length, i = 0; + + if ( isArrayLike( obj ) ) { + length = obj.length; + for ( ; i < length; i++ ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } else { + for ( i in obj ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } + + return obj; + }, + + // results is for internal usage only + makeArray: function( arr, results ) { + var ret = results || []; + + if ( arr != null ) { + if ( isArrayLike( Object( arr ) ) ) { + jQuery.merge( ret, + typeof arr === "string" ? + [ arr ] : arr + ); + } else { + push.call( ret, arr ); + } + } + + return ret; + }, + + inArray: function( elem, arr, i ) { + return arr == null ? -1 : indexOf.call( arr, elem, i ); + }, + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + merge: function( first, second ) { + var len = +second.length, + j = 0, + i = first.length; + + for ( ; j < len; j++ ) { + first[ i++ ] = second[ j ]; + } + + first.length = i; + + return first; + }, + + grep: function( elems, callback, invert ) { + var callbackInverse, + matches = [], + i = 0, + length = elems.length, + callbackExpect = !invert; + + // Go through the array, only saving the items + // that pass the validator function + for ( ; i < length; i++ ) { + callbackInverse = !callback( elems[ i ], i ); + if ( callbackInverse !== callbackExpect ) { + matches.push( elems[ i ] ); + } + } + + return matches; + }, + + // arg is for internal usage only + map: function( elems, callback, arg ) { + var length, value, + i = 0, + ret = []; + + // Go through the array, translating each of the items to their new values + if ( isArrayLike( elems ) ) { + length = elems.length; + for ( ; i < length; i++ ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + + // Go through every key on the object, + } else { + for ( i in elems ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + } + + // Flatten any nested arrays + return flat( ret ); + }, + + // A global GUID counter for objects + guid: 1, + + // jQuery.support is not used in Core but other projects attach their + // properties to it so it needs to exist. + support: support +} ); + +if ( typeof Symbol === "function" ) { + jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ]; +} + +// Populate the class2type map +jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ), + function( _i, name ) { + class2type[ "[object " + name + "]" ] = name.toLowerCase(); + } ); + +function isArrayLike( obj ) { + + // Support: real iOS 8.2 only (not reproducible in simulator) + // `in` check used to prevent JIT error (gh-2145) + // hasOwn isn't used here due to false negatives + // regarding Nodelist length in IE + var length = !!obj && "length" in obj && obj.length, + type = toType( obj ); + + if ( isFunction( obj ) || isWindow( obj ) ) { + return false; + } + + return type === "array" || length === 0 || + typeof length === "number" && length > 0 && ( length - 1 ) in obj; +} +var Sizzle = +/*! + * Sizzle CSS Selector Engine v2.3.6 + * https://sizzlejs.com/ + * + * Copyright JS Foundation and other contributors + * Released under the MIT license + * https://js.foundation/ + * + * Date: 2021-02-16 + */ +( function( window ) { +var i, + support, + Expr, + getText, + isXML, + tokenize, + compile, + select, + outermostContext, + sortInput, + hasDuplicate, + + // Local document vars + setDocument, + document, + docElem, + documentIsHTML, + rbuggyQSA, + rbuggyMatches, + matches, + contains, + + // Instance-specific data + expando = "sizzle" + 1 * new Date(), + preferredDoc = window.document, + dirruns = 0, + done = 0, + classCache = createCache(), + tokenCache = createCache(), + compilerCache = createCache(), + nonnativeSelectorCache = createCache(), + sortOrder = function( a, b ) { + if ( a === b ) { + hasDuplicate = true; + } + return 0; + }, + + // Instance methods + hasOwn = ( {} ).hasOwnProperty, + arr = [], + pop = arr.pop, + pushNative = arr.push, + push = arr.push, + slice = arr.slice, + + // Use a stripped-down indexOf as it's faster than native + // https://jsperf.com/thor-indexof-vs-for/5 + indexOf = function( list, elem ) { + var i = 0, + len = list.length; + for ( ; i < len; i++ ) { + if ( list[ i ] === elem ) { + return i; + } + } + return -1; + }, + + booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|" + + "ismap|loop|multiple|open|readonly|required|scoped", + + // Regular expressions + + // http://www.w3.org/TR/css3-selectors/#whitespace + whitespace = "[\\x20\\t\\r\\n\\f]", + + // https://www.w3.org/TR/css-syntax-3/#ident-token-diagram + identifier = "(?:\\\\[\\da-fA-F]{1,6}" + whitespace + + "?|\\\\[^\\r\\n\\f]|[\\w-]|[^\0-\\x7f])+", + + // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors + attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + + + // Operator (capture 2) + "*([*^$|!~]?=)" + whitespace + + + // "Attribute values must be CSS identifiers [capture 5] + // or strings [capture 3 or capture 4]" + "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + + whitespace + "*\\]", + + pseudos = ":(" + identifier + ")(?:\\((" + + + // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: + // 1. quoted (capture 3; capture 4 or capture 5) + "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + + + // 2. simple (capture 6) + "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + + + // 3. anything else (capture 2) + ".*" + + ")\\)|)", + + // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter + rwhitespace = new RegExp( whitespace + "+", "g" ), + rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + + whitespace + "+$", "g" ), + + rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), + rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + + "*" ), + rdescend = new RegExp( whitespace + "|>" ), + + rpseudo = new RegExp( pseudos ), + ridentifier = new RegExp( "^" + identifier + "$" ), + + matchExpr = { + "ID": new RegExp( "^#(" + identifier + ")" ), + "CLASS": new RegExp( "^\\.(" + identifier + ")" ), + "TAG": new RegExp( "^(" + identifier + "|[*])" ), + "ATTR": new RegExp( "^" + attributes ), + "PSEUDO": new RegExp( "^" + pseudos ), + "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + + whitespace + "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + + whitespace + "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), + "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), + + // For use in libraries implementing .is() + // We use this for POS matching in `select` + "needsContext": new RegExp( "^" + whitespace + + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + whitespace + + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) + }, + + rhtml = /HTML$/i, + rinputs = /^(?:input|select|textarea|button)$/i, + rheader = /^h\d$/i, + + rnative = /^[^{]+\{\s*\[native \w/, + + // Easily-parseable/retrievable ID or TAG or CLASS selectors + rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, + + rsibling = /[+~]/, + + // CSS escapes + // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters + runescape = new RegExp( "\\\\[\\da-fA-F]{1,6}" + whitespace + "?|\\\\([^\\r\\n\\f])", "g" ), + funescape = function( escape, nonHex ) { + var high = "0x" + escape.slice( 1 ) - 0x10000; + + return nonHex ? + + // Strip the backslash prefix from a non-hex escape sequence + nonHex : + + // Replace a hexadecimal escape sequence with the encoded Unicode code point + // Support: IE <=11+ + // For values outside the Basic Multilingual Plane (BMP), manually construct a + // surrogate pair + high < 0 ? + String.fromCharCode( high + 0x10000 ) : + String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); + }, + + // CSS string/identifier serialization + // https://drafts.csswg.org/cssom/#common-serializing-idioms + rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g, + fcssescape = function( ch, asCodePoint ) { + if ( asCodePoint ) { + + // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER + if ( ch === "\0" ) { + return "\uFFFD"; + } + + // Control characters and (dependent upon position) numbers get escaped as code points + return ch.slice( 0, -1 ) + "\\" + + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " "; + } + + // Other potentially-special ASCII characters get backslash-escaped + return "\\" + ch; + }, + + // Used for iframes + // See setDocument() + // Removing the function wrapper causes a "Permission Denied" + // error in IE + unloadHandler = function() { + setDocument(); + }, + + inDisabledFieldset = addCombinator( + function( elem ) { + return elem.disabled === true && elem.nodeName.toLowerCase() === "fieldset"; + }, + { dir: "parentNode", next: "legend" } + ); + +// Optimize for push.apply( _, NodeList ) +try { + push.apply( + ( arr = slice.call( preferredDoc.childNodes ) ), + preferredDoc.childNodes + ); + + // Support: Android<4.0 + // Detect silently failing push.apply + // eslint-disable-next-line no-unused-expressions + arr[ preferredDoc.childNodes.length ].nodeType; +} catch ( e ) { + push = { apply: arr.length ? + + // Leverage slice if possible + function( target, els ) { + pushNative.apply( target, slice.call( els ) ); + } : + + // Support: IE<9 + // Otherwise append directly + function( target, els ) { + var j = target.length, + i = 0; + + // Can't trust NodeList.length + while ( ( target[ j++ ] = els[ i++ ] ) ) {} + target.length = j - 1; + } + }; +} + +function Sizzle( selector, context, results, seed ) { + var m, i, elem, nid, match, groups, newSelector, + newContext = context && context.ownerDocument, + + // nodeType defaults to 9, since context defaults to document + nodeType = context ? context.nodeType : 9; + + results = results || []; + + // Return early from calls with invalid selector or context + if ( typeof selector !== "string" || !selector || + nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { + + return results; + } + + // Try to shortcut find operations (as opposed to filters) in HTML documents + if ( !seed ) { + setDocument( context ); + context = context || document; + + if ( documentIsHTML ) { + + // If the selector is sufficiently simple, try using a "get*By*" DOM method + // (excepting DocumentFragment context, where the methods don't exist) + if ( nodeType !== 11 && ( match = rquickExpr.exec( selector ) ) ) { + + // ID selector + if ( ( m = match[ 1 ] ) ) { + + // Document context + if ( nodeType === 9 ) { + if ( ( elem = context.getElementById( m ) ) ) { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( elem.id === m ) { + results.push( elem ); + return results; + } + } else { + return results; + } + + // Element context + } else { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( newContext && ( elem = newContext.getElementById( m ) ) && + contains( context, elem ) && + elem.id === m ) { + + results.push( elem ); + return results; + } + } + + // Type selector + } else if ( match[ 2 ] ) { + push.apply( results, context.getElementsByTagName( selector ) ); + return results; + + // Class selector + } else if ( ( m = match[ 3 ] ) && support.getElementsByClassName && + context.getElementsByClassName ) { + + push.apply( results, context.getElementsByClassName( m ) ); + return results; + } + } + + // Take advantage of querySelectorAll + if ( support.qsa && + !nonnativeSelectorCache[ selector + " " ] && + ( !rbuggyQSA || !rbuggyQSA.test( selector ) ) && + + // Support: IE 8 only + // Exclude object elements + ( nodeType !== 1 || context.nodeName.toLowerCase() !== "object" ) ) { + + newSelector = selector; + newContext = context; + + // qSA considers elements outside a scoping root when evaluating child or + // descendant combinators, which is not what we want. + // In such cases, we work around the behavior by prefixing every selector in the + // list with an ID selector referencing the scope context. + // The technique has to be used as well when a leading combinator is used + // as such selectors are not recognized by querySelectorAll. + // Thanks to Andrew Dupont for this technique. + if ( nodeType === 1 && + ( rdescend.test( selector ) || rcombinators.test( selector ) ) ) { + + // Expand context for sibling selectors + newContext = rsibling.test( selector ) && testContext( context.parentNode ) || + context; + + // We can use :scope instead of the ID hack if the browser + // supports it & if we're not changing the context. + if ( newContext !== context || !support.scope ) { + + // Capture the context ID, setting it first if necessary + if ( ( nid = context.getAttribute( "id" ) ) ) { + nid = nid.replace( rcssescape, fcssescape ); + } else { + context.setAttribute( "id", ( nid = expando ) ); + } + } + + // Prefix every selector in the list + groups = tokenize( selector ); + i = groups.length; + while ( i-- ) { + groups[ i ] = ( nid ? "#" + nid : ":scope" ) + " " + + toSelector( groups[ i ] ); + } + newSelector = groups.join( "," ); + } + + try { + push.apply( results, + newContext.querySelectorAll( newSelector ) + ); + return results; + } catch ( qsaError ) { + nonnativeSelectorCache( selector, true ); + } finally { + if ( nid === expando ) { + context.removeAttribute( "id" ); + } + } + } + } + } + + // All others + return select( selector.replace( rtrim, "$1" ), context, results, seed ); +} + +/** + * Create key-value caches of limited size + * @returns {function(string, object)} Returns the Object data after storing it on itself with + * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) + * deleting the oldest entry + */ +function createCache() { + var keys = []; + + function cache( key, value ) { + + // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) + if ( keys.push( key + " " ) > Expr.cacheLength ) { + + // Only keep the most recent entries + delete cache[ keys.shift() ]; + } + return ( cache[ key + " " ] = value ); + } + return cache; +} + +/** + * Mark a function for special use by Sizzle + * @param {Function} fn The function to mark + */ +function markFunction( fn ) { + fn[ expando ] = true; + return fn; +} + +/** + * Support testing using an element + * @param {Function} fn Passed the created element and returns a boolean result + */ +function assert( fn ) { + var el = document.createElement( "fieldset" ); + + try { + return !!fn( el ); + } catch ( e ) { + return false; + } finally { + + // Remove from its parent by default + if ( el.parentNode ) { + el.parentNode.removeChild( el ); + } + + // release memory in IE + el = null; + } +} + +/** + * Adds the same handler for all of the specified attrs + * @param {String} attrs Pipe-separated list of attributes + * @param {Function} handler The method that will be applied + */ +function addHandle( attrs, handler ) { + var arr = attrs.split( "|" ), + i = arr.length; + + while ( i-- ) { + Expr.attrHandle[ arr[ i ] ] = handler; + } +} + +/** + * Checks document order of two siblings + * @param {Element} a + * @param {Element} b + * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b + */ +function siblingCheck( a, b ) { + var cur = b && a, + diff = cur && a.nodeType === 1 && b.nodeType === 1 && + a.sourceIndex - b.sourceIndex; + + // Use IE sourceIndex if available on both nodes + if ( diff ) { + return diff; + } + + // Check if b follows a + if ( cur ) { + while ( ( cur = cur.nextSibling ) ) { + if ( cur === b ) { + return -1; + } + } + } + + return a ? 1 : -1; +} + +/** + * Returns a function to use in pseudos for input types + * @param {String} type + */ +function createInputPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for buttons + * @param {String} type + */ +function createButtonPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return ( name === "input" || name === "button" ) && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for :enabled/:disabled + * @param {Boolean} disabled true for :disabled; false for :enabled + */ +function createDisabledPseudo( disabled ) { + + // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable + return function( elem ) { + + // Only certain elements can match :enabled or :disabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled + if ( "form" in elem ) { + + // Check for inherited disabledness on relevant non-disabled elements: + // * listed form-associated elements in a disabled fieldset + // https://html.spec.whatwg.org/multipage/forms.html#category-listed + // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled + // * option elements in a disabled optgroup + // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled + // All such elements have a "form" property. + if ( elem.parentNode && elem.disabled === false ) { + + // Option elements defer to a parent optgroup if present + if ( "label" in elem ) { + if ( "label" in elem.parentNode ) { + return elem.parentNode.disabled === disabled; + } else { + return elem.disabled === disabled; + } + } + + // Support: IE 6 - 11 + // Use the isDisabled shortcut property to check for disabled fieldset ancestors + return elem.isDisabled === disabled || + + // Where there is no isDisabled, check manually + /* jshint -W018 */ + elem.isDisabled !== !disabled && + inDisabledFieldset( elem ) === disabled; + } + + return elem.disabled === disabled; + + // Try to winnow out elements that can't be disabled before trusting the disabled property. + // Some victims get caught in our net (label, legend, menu, track), but it shouldn't + // even exist on them, let alone have a boolean value. + } else if ( "label" in elem ) { + return elem.disabled === disabled; + } + + // Remaining elements are neither :enabled nor :disabled + return false; + }; +} + +/** + * Returns a function to use in pseudos for positionals + * @param {Function} fn + */ +function createPositionalPseudo( fn ) { + return markFunction( function( argument ) { + argument = +argument; + return markFunction( function( seed, matches ) { + var j, + matchIndexes = fn( [], seed.length, argument ), + i = matchIndexes.length; + + // Match elements found at the specified indexes + while ( i-- ) { + if ( seed[ ( j = matchIndexes[ i ] ) ] ) { + seed[ j ] = !( matches[ j ] = seed[ j ] ); + } + } + } ); + } ); +} + +/** + * Checks a node for validity as a Sizzle context + * @param {Element|Object=} context + * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value + */ +function testContext( context ) { + return context && typeof context.getElementsByTagName !== "undefined" && context; +} + +// Expose support vars for convenience +support = Sizzle.support = {}; + +/** + * Detects XML nodes + * @param {Element|Object} elem An element or a document + * @returns {Boolean} True iff elem is a non-HTML XML node + */ +isXML = Sizzle.isXML = function( elem ) { + var namespace = elem && elem.namespaceURI, + docElem = elem && ( elem.ownerDocument || elem ).documentElement; + + // Support: IE <=8 + // Assume HTML when documentElement doesn't yet exist, such as inside loading iframes + // https://bugs.jquery.com/ticket/4833 + return !rhtml.test( namespace || docElem && docElem.nodeName || "HTML" ); +}; + +/** + * Sets document-related variables once based on the current document + * @param {Element|Object} [doc] An element or document object to use to set the document + * @returns {Object} Returns the current document + */ +setDocument = Sizzle.setDocument = function( node ) { + var hasCompare, subWindow, + doc = node ? node.ownerDocument || node : preferredDoc; + + // Return early if doc is invalid or already selected + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( doc == document || doc.nodeType !== 9 || !doc.documentElement ) { + return document; + } + + // Update global variables + document = doc; + docElem = document.documentElement; + documentIsHTML = !isXML( document ); + + // Support: IE 9 - 11+, Edge 12 - 18+ + // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936) + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( preferredDoc != document && + ( subWindow = document.defaultView ) && subWindow.top !== subWindow ) { + + // Support: IE 11, Edge + if ( subWindow.addEventListener ) { + subWindow.addEventListener( "unload", unloadHandler, false ); + + // Support: IE 9 - 10 only + } else if ( subWindow.attachEvent ) { + subWindow.attachEvent( "onunload", unloadHandler ); + } + } + + // Support: IE 8 - 11+, Edge 12 - 18+, Chrome <=16 - 25 only, Firefox <=3.6 - 31 only, + // Safari 4 - 5 only, Opera <=11.6 - 12.x only + // IE/Edge & older browsers don't support the :scope pseudo-class. + // Support: Safari 6.0 only + // Safari 6.0 supports :scope but it's an alias of :root there. + support.scope = assert( function( el ) { + docElem.appendChild( el ).appendChild( document.createElement( "div" ) ); + return typeof el.querySelectorAll !== "undefined" && + !el.querySelectorAll( ":scope fieldset div" ).length; + } ); + + /* Attributes + ---------------------------------------------------------------------- */ + + // Support: IE<8 + // Verify that getAttribute really returns attributes and not properties + // (excepting IE8 booleans) + support.attributes = assert( function( el ) { + el.className = "i"; + return !el.getAttribute( "className" ); + } ); + + /* getElement(s)By* + ---------------------------------------------------------------------- */ + + // Check if getElementsByTagName("*") returns only elements + support.getElementsByTagName = assert( function( el ) { + el.appendChild( document.createComment( "" ) ); + return !el.getElementsByTagName( "*" ).length; + } ); + + // Support: IE<9 + support.getElementsByClassName = rnative.test( document.getElementsByClassName ); + + // Support: IE<10 + // Check if getElementById returns elements by name + // The broken getElementById methods don't pick up programmatically-set names, + // so use a roundabout getElementsByName test + support.getById = assert( function( el ) { + docElem.appendChild( el ).id = expando; + return !document.getElementsByName || !document.getElementsByName( expando ).length; + } ); + + // ID filter and find + if ( support.getById ) { + Expr.filter[ "ID" ] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + return elem.getAttribute( "id" ) === attrId; + }; + }; + Expr.find[ "ID" ] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var elem = context.getElementById( id ); + return elem ? [ elem ] : []; + } + }; + } else { + Expr.filter[ "ID" ] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + var node = typeof elem.getAttributeNode !== "undefined" && + elem.getAttributeNode( "id" ); + return node && node.value === attrId; + }; + }; + + // Support: IE 6 - 7 only + // getElementById is not reliable as a find shortcut + Expr.find[ "ID" ] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var node, i, elems, + elem = context.getElementById( id ); + + if ( elem ) { + + // Verify the id attribute + node = elem.getAttributeNode( "id" ); + if ( node && node.value === id ) { + return [ elem ]; + } + + // Fall back on getElementsByName + elems = context.getElementsByName( id ); + i = 0; + while ( ( elem = elems[ i++ ] ) ) { + node = elem.getAttributeNode( "id" ); + if ( node && node.value === id ) { + return [ elem ]; + } + } + } + + return []; + } + }; + } + + // Tag + Expr.find[ "TAG" ] = support.getElementsByTagName ? + function( tag, context ) { + if ( typeof context.getElementsByTagName !== "undefined" ) { + return context.getElementsByTagName( tag ); + + // DocumentFragment nodes don't have gEBTN + } else if ( support.qsa ) { + return context.querySelectorAll( tag ); + } + } : + + function( tag, context ) { + var elem, + tmp = [], + i = 0, + + // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too + results = context.getElementsByTagName( tag ); + + // Filter out possible comments + if ( tag === "*" ) { + while ( ( elem = results[ i++ ] ) ) { + if ( elem.nodeType === 1 ) { + tmp.push( elem ); + } + } + + return tmp; + } + return results; + }; + + // Class + Expr.find[ "CLASS" ] = support.getElementsByClassName && function( className, context ) { + if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) { + return context.getElementsByClassName( className ); + } + }; + + /* QSA/matchesSelector + ---------------------------------------------------------------------- */ + + // QSA and matchesSelector support + + // matchesSelector(:active) reports false when true (IE9/Opera 11.5) + rbuggyMatches = []; + + // qSa(:focus) reports false when true (Chrome 21) + // We allow this because of a bug in IE8/9 that throws an error + // whenever `document.activeElement` is accessed on an iframe + // So, we allow :focus to pass through QSA all the time to avoid the IE error + // See https://bugs.jquery.com/ticket/13378 + rbuggyQSA = []; + + if ( ( support.qsa = rnative.test( document.querySelectorAll ) ) ) { + + // Build QSA regex + // Regex strategy adopted from Diego Perini + assert( function( el ) { + + var input; + + // Select is set to empty string on purpose + // This is to test IE's treatment of not explicitly + // setting a boolean content attribute, + // since its presence should be enough + // https://bugs.jquery.com/ticket/12359 + docElem.appendChild( el ).innerHTML = "" + + ""; + + // Support: IE8, Opera 11-12.16 + // Nothing should be selected when empty strings follow ^= or $= or *= + // The test attribute must be unknown in Opera but "safe" for WinRT + // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section + if ( el.querySelectorAll( "[msallowcapture^='']" ).length ) { + rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); + } + + // Support: IE8 + // Boolean attributes and "value" are not treated correctly + if ( !el.querySelectorAll( "[selected]" ).length ) { + rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); + } + + // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+ + if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) { + rbuggyQSA.push( "~=" ); + } + + // Support: IE 11+, Edge 15 - 18+ + // IE 11/Edge don't find elements on a `[name='']` query in some cases. + // Adding a temporary attribute to the document before the selection works + // around the issue. + // Interestingly, IE 10 & older don't seem to have the issue. + input = document.createElement( "input" ); + input.setAttribute( "name", "" ); + el.appendChild( input ); + if ( !el.querySelectorAll( "[name='']" ).length ) { + rbuggyQSA.push( "\\[" + whitespace + "*name" + whitespace + "*=" + + whitespace + "*(?:''|\"\")" ); + } + + // Webkit/Opera - :checked should return selected option elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + // IE8 throws error here and will not see later tests + if ( !el.querySelectorAll( ":checked" ).length ) { + rbuggyQSA.push( ":checked" ); + } + + // Support: Safari 8+, iOS 8+ + // https://bugs.webkit.org/show_bug.cgi?id=136851 + // In-page `selector#id sibling-combinator selector` fails + if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) { + rbuggyQSA.push( ".#.+[+~]" ); + } + + // Support: Firefox <=3.6 - 5 only + // Old Firefox doesn't throw on a badly-escaped identifier. + el.querySelectorAll( "\\\f" ); + rbuggyQSA.push( "[\\r\\n\\f]" ); + } ); + + assert( function( el ) { + el.innerHTML = "" + + ""; + + // Support: Windows 8 Native Apps + // The type and name attributes are restricted during .innerHTML assignment + var input = document.createElement( "input" ); + input.setAttribute( "type", "hidden" ); + el.appendChild( input ).setAttribute( "name", "D" ); + + // Support: IE8 + // Enforce case-sensitivity of name attribute + if ( el.querySelectorAll( "[name=d]" ).length ) { + rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" ); + } + + // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled) + // IE8 throws error here and will not see later tests + if ( el.querySelectorAll( ":enabled" ).length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: IE9-11+ + // IE's :disabled selector does not pick up the children of disabled fieldsets + docElem.appendChild( el ).disabled = true; + if ( el.querySelectorAll( ":disabled" ).length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: Opera 10 - 11 only + // Opera 10-11 does not throw on post-comma invalid pseudos + el.querySelectorAll( "*,:x" ); + rbuggyQSA.push( ",.*:" ); + } ); + } + + if ( ( support.matchesSelector = rnative.test( ( matches = docElem.matches || + docElem.webkitMatchesSelector || + docElem.mozMatchesSelector || + docElem.oMatchesSelector || + docElem.msMatchesSelector ) ) ) ) { + + assert( function( el ) { + + // Check to see if it's possible to do matchesSelector + // on a disconnected node (IE 9) + support.disconnectedMatch = matches.call( el, "*" ); + + // This should fail with an exception + // Gecko does not error, returns false instead + matches.call( el, "[s!='']:x" ); + rbuggyMatches.push( "!=", pseudos ); + } ); + } + + rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join( "|" ) ); + rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join( "|" ) ); + + /* Contains + ---------------------------------------------------------------------- */ + hasCompare = rnative.test( docElem.compareDocumentPosition ); + + // Element contains another + // Purposefully self-exclusive + // As in, an element does not contain itself + contains = hasCompare || rnative.test( docElem.contains ) ? + function( a, b ) { + var adown = a.nodeType === 9 ? a.documentElement : a, + bup = b && b.parentNode; + return a === bup || !!( bup && bup.nodeType === 1 && ( + adown.contains ? + adown.contains( bup ) : + a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16 + ) ); + } : + function( a, b ) { + if ( b ) { + while ( ( b = b.parentNode ) ) { + if ( b === a ) { + return true; + } + } + } + return false; + }; + + /* Sorting + ---------------------------------------------------------------------- */ + + // Document order sorting + sortOrder = hasCompare ? + function( a, b ) { + + // Flag for duplicate removal + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + // Sort on method existence if only one input has compareDocumentPosition + var compare = !a.compareDocumentPosition - !b.compareDocumentPosition; + if ( compare ) { + return compare; + } + + // Calculate position if both inputs belong to the same document + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + compare = ( a.ownerDocument || a ) == ( b.ownerDocument || b ) ? + a.compareDocumentPosition( b ) : + + // Otherwise we know they are disconnected + 1; + + // Disconnected nodes + if ( compare & 1 || + ( !support.sortDetached && b.compareDocumentPosition( a ) === compare ) ) { + + // Choose the first element that is related to our preferred document + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( a == document || a.ownerDocument == preferredDoc && + contains( preferredDoc, a ) ) { + return -1; + } + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( b == document || b.ownerDocument == preferredDoc && + contains( preferredDoc, b ) ) { + return 1; + } + + // Maintain original order + return sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + } + + return compare & 4 ? -1 : 1; + } : + function( a, b ) { + + // Exit early if the nodes are identical + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + var cur, + i = 0, + aup = a.parentNode, + bup = b.parentNode, + ap = [ a ], + bp = [ b ]; + + // Parentless nodes are either documents or disconnected + if ( !aup || !bup ) { + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + /* eslint-disable eqeqeq */ + return a == document ? -1 : + b == document ? 1 : + /* eslint-enable eqeqeq */ + aup ? -1 : + bup ? 1 : + sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + + // If the nodes are siblings, we can do a quick check + } else if ( aup === bup ) { + return siblingCheck( a, b ); + } + + // Otherwise we need full lists of their ancestors for comparison + cur = a; + while ( ( cur = cur.parentNode ) ) { + ap.unshift( cur ); + } + cur = b; + while ( ( cur = cur.parentNode ) ) { + bp.unshift( cur ); + } + + // Walk down the tree looking for a discrepancy + while ( ap[ i ] === bp[ i ] ) { + i++; + } + + return i ? + + // Do a sibling check if the nodes have a common ancestor + siblingCheck( ap[ i ], bp[ i ] ) : + + // Otherwise nodes in our document sort first + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + /* eslint-disable eqeqeq */ + ap[ i ] == preferredDoc ? -1 : + bp[ i ] == preferredDoc ? 1 : + /* eslint-enable eqeqeq */ + 0; + }; + + return document; +}; + +Sizzle.matches = function( expr, elements ) { + return Sizzle( expr, null, null, elements ); +}; + +Sizzle.matchesSelector = function( elem, expr ) { + setDocument( elem ); + + if ( support.matchesSelector && documentIsHTML && + !nonnativeSelectorCache[ expr + " " ] && + ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) && + ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) { + + try { + var ret = matches.call( elem, expr ); + + // IE 9's matchesSelector returns false on disconnected nodes + if ( ret || support.disconnectedMatch || + + // As well, disconnected nodes are said to be in a document + // fragment in IE 9 + elem.document && elem.document.nodeType !== 11 ) { + return ret; + } + } catch ( e ) { + nonnativeSelectorCache( expr, true ); + } + } + + return Sizzle( expr, document, null, [ elem ] ).length > 0; +}; + +Sizzle.contains = function( context, elem ) { + + // Set document vars if needed + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( ( context.ownerDocument || context ) != document ) { + setDocument( context ); + } + return contains( context, elem ); +}; + +Sizzle.attr = function( elem, name ) { + + // Set document vars if needed + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( ( elem.ownerDocument || elem ) != document ) { + setDocument( elem ); + } + + var fn = Expr.attrHandle[ name.toLowerCase() ], + + // Don't get fooled by Object.prototype properties (jQuery #13807) + val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ? + fn( elem, name, !documentIsHTML ) : + undefined; + + return val !== undefined ? + val : + support.attributes || !documentIsHTML ? + elem.getAttribute( name ) : + ( val = elem.getAttributeNode( name ) ) && val.specified ? + val.value : + null; +}; + +Sizzle.escape = function( sel ) { + return ( sel + "" ).replace( rcssescape, fcssescape ); +}; + +Sizzle.error = function( msg ) { + throw new Error( "Syntax error, unrecognized expression: " + msg ); +}; + +/** + * Document sorting and removing duplicates + * @param {ArrayLike} results + */ +Sizzle.uniqueSort = function( results ) { + var elem, + duplicates = [], + j = 0, + i = 0; + + // Unless we *know* we can detect duplicates, assume their presence + hasDuplicate = !support.detectDuplicates; + sortInput = !support.sortStable && results.slice( 0 ); + results.sort( sortOrder ); + + if ( hasDuplicate ) { + while ( ( elem = results[ i++ ] ) ) { + if ( elem === results[ i ] ) { + j = duplicates.push( i ); + } + } + while ( j-- ) { + results.splice( duplicates[ j ], 1 ); + } + } + + // Clear input after sorting to release objects + // See https://github.com/jquery/sizzle/pull/225 + sortInput = null; + + return results; +}; + +/** + * Utility function for retrieving the text value of an array of DOM nodes + * @param {Array|Element} elem + */ +getText = Sizzle.getText = function( elem ) { + var node, + ret = "", + i = 0, + nodeType = elem.nodeType; + + if ( !nodeType ) { + + // If no nodeType, this is expected to be an array + while ( ( node = elem[ i++ ] ) ) { + + // Do not traverse comment nodes + ret += getText( node ); + } + } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { + + // Use textContent for elements + // innerText usage removed for consistency of new lines (jQuery #11153) + if ( typeof elem.textContent === "string" ) { + return elem.textContent; + } else { + + // Traverse its children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + ret += getText( elem ); + } + } + } else if ( nodeType === 3 || nodeType === 4 ) { + return elem.nodeValue; + } + + // Do not include comment or processing instruction nodes + + return ret; +}; + +Expr = Sizzle.selectors = { + + // Can be adjusted by the user + cacheLength: 50, + + createPseudo: markFunction, + + match: matchExpr, + + attrHandle: {}, + + find: {}, + + relative: { + ">": { dir: "parentNode", first: true }, + " ": { dir: "parentNode" }, + "+": { dir: "previousSibling", first: true }, + "~": { dir: "previousSibling" } + }, + + preFilter: { + "ATTR": function( match ) { + match[ 1 ] = match[ 1 ].replace( runescape, funescape ); + + // Move the given value to match[3] whether quoted or unquoted + match[ 3 ] = ( match[ 3 ] || match[ 4 ] || + match[ 5 ] || "" ).replace( runescape, funescape ); + + if ( match[ 2 ] === "~=" ) { + match[ 3 ] = " " + match[ 3 ] + " "; + } + + return match.slice( 0, 4 ); + }, + + "CHILD": function( match ) { + + /* matches from matchExpr["CHILD"] + 1 type (only|nth|...) + 2 what (child|of-type) + 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...) + 4 xn-component of xn+y argument ([+-]?\d*n|) + 5 sign of xn-component + 6 x of xn-component + 7 sign of y-component + 8 y of y-component + */ + match[ 1 ] = match[ 1 ].toLowerCase(); + + if ( match[ 1 ].slice( 0, 3 ) === "nth" ) { + + // nth-* requires argument + if ( !match[ 3 ] ) { + Sizzle.error( match[ 0 ] ); + } + + // numeric x and y parameters for Expr.filter.CHILD + // remember that false/true cast respectively to 0/1 + match[ 4 ] = +( match[ 4 ] ? + match[ 5 ] + ( match[ 6 ] || 1 ) : + 2 * ( match[ 3 ] === "even" || match[ 3 ] === "odd" ) ); + match[ 5 ] = +( ( match[ 7 ] + match[ 8 ] ) || match[ 3 ] === "odd" ); + + // other types prohibit arguments + } else if ( match[ 3 ] ) { + Sizzle.error( match[ 0 ] ); + } + + return match; + }, + + "PSEUDO": function( match ) { + var excess, + unquoted = !match[ 6 ] && match[ 2 ]; + + if ( matchExpr[ "CHILD" ].test( match[ 0 ] ) ) { + return null; + } + + // Accept quoted arguments as-is + if ( match[ 3 ] ) { + match[ 2 ] = match[ 4 ] || match[ 5 ] || ""; + + // Strip excess characters from unquoted arguments + } else if ( unquoted && rpseudo.test( unquoted ) && + + // Get excess from tokenize (recursively) + ( excess = tokenize( unquoted, true ) ) && + + // advance to the next closing parenthesis + ( excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length ) ) { + + // excess is a negative index + match[ 0 ] = match[ 0 ].slice( 0, excess ); + match[ 2 ] = unquoted.slice( 0, excess ); + } + + // Return only captures needed by the pseudo filter method (type and argument) + return match.slice( 0, 3 ); + } + }, + + filter: { + + "TAG": function( nodeNameSelector ) { + var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase(); + return nodeNameSelector === "*" ? + function() { + return true; + } : + function( elem ) { + return elem.nodeName && elem.nodeName.toLowerCase() === nodeName; + }; + }, + + "CLASS": function( className ) { + var pattern = classCache[ className + " " ]; + + return pattern || + ( pattern = new RegExp( "(^|" + whitespace + + ")" + className + "(" + whitespace + "|$)" ) ) && classCache( + className, function( elem ) { + return pattern.test( + typeof elem.className === "string" && elem.className || + typeof elem.getAttribute !== "undefined" && + elem.getAttribute( "class" ) || + "" + ); + } ); + }, + + "ATTR": function( name, operator, check ) { + return function( elem ) { + var result = Sizzle.attr( elem, name ); + + if ( result == null ) { + return operator === "!="; + } + if ( !operator ) { + return true; + } + + result += ""; + + /* eslint-disable max-len */ + + return operator === "=" ? result === check : + operator === "!=" ? result !== check : + operator === "^=" ? check && result.indexOf( check ) === 0 : + operator === "*=" ? check && result.indexOf( check ) > -1 : + operator === "$=" ? check && result.slice( -check.length ) === check : + operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 : + operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : + false; + /* eslint-enable max-len */ + + }; + }, + + "CHILD": function( type, what, _argument, first, last ) { + var simple = type.slice( 0, 3 ) !== "nth", + forward = type.slice( -4 ) !== "last", + ofType = what === "of-type"; + + return first === 1 && last === 0 ? + + // Shortcut for :nth-*(n) + function( elem ) { + return !!elem.parentNode; + } : + + function( elem, _context, xml ) { + var cache, uniqueCache, outerCache, node, nodeIndex, start, + dir = simple !== forward ? "nextSibling" : "previousSibling", + parent = elem.parentNode, + name = ofType && elem.nodeName.toLowerCase(), + useCache = !xml && !ofType, + diff = false; + + if ( parent ) { + + // :(first|last|only)-(child|of-type) + if ( simple ) { + while ( dir ) { + node = elem; + while ( ( node = node[ dir ] ) ) { + if ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) { + + return false; + } + } + + // Reverse direction for :only-* (if we haven't yet done so) + start = dir = type === "only" && !start && "nextSibling"; + } + return true; + } + + start = [ forward ? parent.firstChild : parent.lastChild ]; + + // non-xml :nth-child(...) stores cache data on `parent` + if ( forward && useCache ) { + + // Seek `elem` from a previously-cached index + + // ...in a gzip-friendly way + node = parent; + outerCache = node[ expando ] || ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex && cache[ 2 ]; + node = nodeIndex && parent.childNodes[ nodeIndex ]; + + while ( ( node = ++nodeIndex && node && node[ dir ] || + + // Fallback to seeking `elem` from the start + ( diff = nodeIndex = 0 ) || start.pop() ) ) { + + // When found, cache indexes on `parent` and break + if ( node.nodeType === 1 && ++diff && node === elem ) { + uniqueCache[ type ] = [ dirruns, nodeIndex, diff ]; + break; + } + } + + } else { + + // Use previously-cached element index if available + if ( useCache ) { + + // ...in a gzip-friendly way + node = elem; + outerCache = node[ expando ] || ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex; + } + + // xml :nth-child(...) + // or :nth-last-child(...) or :nth(-last)?-of-type(...) + if ( diff === false ) { + + // Use the same loop as above to seek `elem` from the start + while ( ( node = ++nodeIndex && node && node[ dir ] || + ( diff = nodeIndex = 0 ) || start.pop() ) ) { + + if ( ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) && + ++diff ) { + + // Cache the index of each encountered element + if ( useCache ) { + outerCache = node[ expando ] || + ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + uniqueCache[ type ] = [ dirruns, diff ]; + } + + if ( node === elem ) { + break; + } + } + } + } + } + + // Incorporate the offset, then check against cycle size + diff -= last; + return diff === first || ( diff % first === 0 && diff / first >= 0 ); + } + }; + }, + + "PSEUDO": function( pseudo, argument ) { + + // pseudo-class names are case-insensitive + // http://www.w3.org/TR/selectors/#pseudo-classes + // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters + // Remember that setFilters inherits from pseudos + var args, + fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] || + Sizzle.error( "unsupported pseudo: " + pseudo ); + + // The user may use createPseudo to indicate that + // arguments are needed to create the filter function + // just as Sizzle does + if ( fn[ expando ] ) { + return fn( argument ); + } + + // But maintain support for old signatures + if ( fn.length > 1 ) { + args = [ pseudo, pseudo, "", argument ]; + return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ? + markFunction( function( seed, matches ) { + var idx, + matched = fn( seed, argument ), + i = matched.length; + while ( i-- ) { + idx = indexOf( seed, matched[ i ] ); + seed[ idx ] = !( matches[ idx ] = matched[ i ] ); + } + } ) : + function( elem ) { + return fn( elem, 0, args ); + }; + } + + return fn; + } + }, + + pseudos: { + + // Potentially complex pseudos + "not": markFunction( function( selector ) { + + // Trim the selector passed to compile + // to avoid treating leading and trailing + // spaces as combinators + var input = [], + results = [], + matcher = compile( selector.replace( rtrim, "$1" ) ); + + return matcher[ expando ] ? + markFunction( function( seed, matches, _context, xml ) { + var elem, + unmatched = matcher( seed, null, xml, [] ), + i = seed.length; + + // Match elements unmatched by `matcher` + while ( i-- ) { + if ( ( elem = unmatched[ i ] ) ) { + seed[ i ] = !( matches[ i ] = elem ); + } + } + } ) : + function( elem, _context, xml ) { + input[ 0 ] = elem; + matcher( input, null, xml, results ); + + // Don't keep the element (issue #299) + input[ 0 ] = null; + return !results.pop(); + }; + } ), + + "has": markFunction( function( selector ) { + return function( elem ) { + return Sizzle( selector, elem ).length > 0; + }; + } ), + + "contains": markFunction( function( text ) { + text = text.replace( runescape, funescape ); + return function( elem ) { + return ( elem.textContent || getText( elem ) ).indexOf( text ) > -1; + }; + } ), + + // "Whether an element is represented by a :lang() selector + // is based solely on the element's language value + // being equal to the identifier C, + // or beginning with the identifier C immediately followed by "-". + // The matching of C against the element's language value is performed case-insensitively. + // The identifier C does not have to be a valid language name." + // http://www.w3.org/TR/selectors/#lang-pseudo + "lang": markFunction( function( lang ) { + + // lang value must be a valid identifier + if ( !ridentifier.test( lang || "" ) ) { + Sizzle.error( "unsupported lang: " + lang ); + } + lang = lang.replace( runescape, funescape ).toLowerCase(); + return function( elem ) { + var elemLang; + do { + if ( ( elemLang = documentIsHTML ? + elem.lang : + elem.getAttribute( "xml:lang" ) || elem.getAttribute( "lang" ) ) ) { + + elemLang = elemLang.toLowerCase(); + return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0; + } + } while ( ( elem = elem.parentNode ) && elem.nodeType === 1 ); + return false; + }; + } ), + + // Miscellaneous + "target": function( elem ) { + var hash = window.location && window.location.hash; + return hash && hash.slice( 1 ) === elem.id; + }, + + "root": function( elem ) { + return elem === docElem; + }, + + "focus": function( elem ) { + return elem === document.activeElement && + ( !document.hasFocus || document.hasFocus() ) && + !!( elem.type || elem.href || ~elem.tabIndex ); + }, + + // Boolean properties + "enabled": createDisabledPseudo( false ), + "disabled": createDisabledPseudo( true ), + + "checked": function( elem ) { + + // In CSS3, :checked should return both checked and selected elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + var nodeName = elem.nodeName.toLowerCase(); + return ( nodeName === "input" && !!elem.checked ) || + ( nodeName === "option" && !!elem.selected ); + }, + + "selected": function( elem ) { + + // Accessing this property makes selected-by-default + // options in Safari work properly + if ( elem.parentNode ) { + // eslint-disable-next-line no-unused-expressions + elem.parentNode.selectedIndex; + } + + return elem.selected === true; + }, + + // Contents + "empty": function( elem ) { + + // http://www.w3.org/TR/selectors/#empty-pseudo + // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5), + // but not by others (comment: 8; processing instruction: 7; etc.) + // nodeType < 6 works because attributes (2) do not appear as children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + if ( elem.nodeType < 6 ) { + return false; + } + } + return true; + }, + + "parent": function( elem ) { + return !Expr.pseudos[ "empty" ]( elem ); + }, + + // Element/input types + "header": function( elem ) { + return rheader.test( elem.nodeName ); + }, + + "input": function( elem ) { + return rinputs.test( elem.nodeName ); + }, + + "button": function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === "button" || name === "button"; + }, + + "text": function( elem ) { + var attr; + return elem.nodeName.toLowerCase() === "input" && + elem.type === "text" && + + // Support: IE<8 + // New HTML5 attribute values (e.g., "search") appear with elem.type === "text" + ( ( attr = elem.getAttribute( "type" ) ) == null || + attr.toLowerCase() === "text" ); + }, + + // Position-in-collection + "first": createPositionalPseudo( function() { + return [ 0 ]; + } ), + + "last": createPositionalPseudo( function( _matchIndexes, length ) { + return [ length - 1 ]; + } ), + + "eq": createPositionalPseudo( function( _matchIndexes, length, argument ) { + return [ argument < 0 ? argument + length : argument ]; + } ), + + "even": createPositionalPseudo( function( matchIndexes, length ) { + var i = 0; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "odd": createPositionalPseudo( function( matchIndexes, length ) { + var i = 1; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "lt": createPositionalPseudo( function( matchIndexes, length, argument ) { + var i = argument < 0 ? + argument + length : + argument > length ? + length : + argument; + for ( ; --i >= 0; ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "gt": createPositionalPseudo( function( matchIndexes, length, argument ) { + var i = argument < 0 ? argument + length : argument; + for ( ; ++i < length; ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ) + } +}; + +Expr.pseudos[ "nth" ] = Expr.pseudos[ "eq" ]; + +// Add button/input type pseudos +for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) { + Expr.pseudos[ i ] = createInputPseudo( i ); +} +for ( i in { submit: true, reset: true } ) { + Expr.pseudos[ i ] = createButtonPseudo( i ); +} + +// Easy API for creating new setFilters +function setFilters() {} +setFilters.prototype = Expr.filters = Expr.pseudos; +Expr.setFilters = new setFilters(); + +tokenize = Sizzle.tokenize = function( selector, parseOnly ) { + var matched, match, tokens, type, + soFar, groups, preFilters, + cached = tokenCache[ selector + " " ]; + + if ( cached ) { + return parseOnly ? 0 : cached.slice( 0 ); + } + + soFar = selector; + groups = []; + preFilters = Expr.preFilter; + + while ( soFar ) { + + // Comma and first run + if ( !matched || ( match = rcomma.exec( soFar ) ) ) { + if ( match ) { + + // Don't consume trailing commas as valid + soFar = soFar.slice( match[ 0 ].length ) || soFar; + } + groups.push( ( tokens = [] ) ); + } + + matched = false; + + // Combinators + if ( ( match = rcombinators.exec( soFar ) ) ) { + matched = match.shift(); + tokens.push( { + value: matched, + + // Cast descendant combinators to space + type: match[ 0 ].replace( rtrim, " " ) + } ); + soFar = soFar.slice( matched.length ); + } + + // Filters + for ( type in Expr.filter ) { + if ( ( match = matchExpr[ type ].exec( soFar ) ) && ( !preFilters[ type ] || + ( match = preFilters[ type ]( match ) ) ) ) { + matched = match.shift(); + tokens.push( { + value: matched, + type: type, + matches: match + } ); + soFar = soFar.slice( matched.length ); + } + } + + if ( !matched ) { + break; + } + } + + // Return the length of the invalid excess + // if we're just parsing + // Otherwise, throw an error or return tokens + return parseOnly ? + soFar.length : + soFar ? + Sizzle.error( selector ) : + + // Cache the tokens + tokenCache( selector, groups ).slice( 0 ); +}; + +function toSelector( tokens ) { + var i = 0, + len = tokens.length, + selector = ""; + for ( ; i < len; i++ ) { + selector += tokens[ i ].value; + } + return selector; +} + +function addCombinator( matcher, combinator, base ) { + var dir = combinator.dir, + skip = combinator.next, + key = skip || dir, + checkNonElements = base && key === "parentNode", + doneName = done++; + + return combinator.first ? + + // Check against closest ancestor/preceding element + function( elem, context, xml ) { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + return matcher( elem, context, xml ); + } + } + return false; + } : + + // Check against all ancestor/preceding elements + function( elem, context, xml ) { + var oldCache, uniqueCache, outerCache, + newCache = [ dirruns, doneName ]; + + // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching + if ( xml ) { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + if ( matcher( elem, context, xml ) ) { + return true; + } + } + } + } else { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + outerCache = elem[ expando ] || ( elem[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ elem.uniqueID ] || + ( outerCache[ elem.uniqueID ] = {} ); + + if ( skip && skip === elem.nodeName.toLowerCase() ) { + elem = elem[ dir ] || elem; + } else if ( ( oldCache = uniqueCache[ key ] ) && + oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) { + + // Assign to newCache so results back-propagate to previous elements + return ( newCache[ 2 ] = oldCache[ 2 ] ); + } else { + + // Reuse newcache so results back-propagate to previous elements + uniqueCache[ key ] = newCache; + + // A match means we're done; a fail means we have to keep checking + if ( ( newCache[ 2 ] = matcher( elem, context, xml ) ) ) { + return true; + } + } + } + } + } + return false; + }; +} + +function elementMatcher( matchers ) { + return matchers.length > 1 ? + function( elem, context, xml ) { + var i = matchers.length; + while ( i-- ) { + if ( !matchers[ i ]( elem, context, xml ) ) { + return false; + } + } + return true; + } : + matchers[ 0 ]; +} + +function multipleContexts( selector, contexts, results ) { + var i = 0, + len = contexts.length; + for ( ; i < len; i++ ) { + Sizzle( selector, contexts[ i ], results ); + } + return results; +} + +function condense( unmatched, map, filter, context, xml ) { + var elem, + newUnmatched = [], + i = 0, + len = unmatched.length, + mapped = map != null; + + for ( ; i < len; i++ ) { + if ( ( elem = unmatched[ i ] ) ) { + if ( !filter || filter( elem, context, xml ) ) { + newUnmatched.push( elem ); + if ( mapped ) { + map.push( i ); + } + } + } + } + + return newUnmatched; +} + +function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) { + if ( postFilter && !postFilter[ expando ] ) { + postFilter = setMatcher( postFilter ); + } + if ( postFinder && !postFinder[ expando ] ) { + postFinder = setMatcher( postFinder, postSelector ); + } + return markFunction( function( seed, results, context, xml ) { + var temp, i, elem, + preMap = [], + postMap = [], + preexisting = results.length, + + // Get initial elements from seed or context + elems = seed || multipleContexts( + selector || "*", + context.nodeType ? [ context ] : context, + [] + ), + + // Prefilter to get matcher input, preserving a map for seed-results synchronization + matcherIn = preFilter && ( seed || !selector ) ? + condense( elems, preMap, preFilter, context, xml ) : + elems, + + matcherOut = matcher ? + + // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results, + postFinder || ( seed ? preFilter : preexisting || postFilter ) ? + + // ...intermediate processing is necessary + [] : + + // ...otherwise use results directly + results : + matcherIn; + + // Find primary matches + if ( matcher ) { + matcher( matcherIn, matcherOut, context, xml ); + } + + // Apply postFilter + if ( postFilter ) { + temp = condense( matcherOut, postMap ); + postFilter( temp, [], context, xml ); + + // Un-match failing elements by moving them back to matcherIn + i = temp.length; + while ( i-- ) { + if ( ( elem = temp[ i ] ) ) { + matcherOut[ postMap[ i ] ] = !( matcherIn[ postMap[ i ] ] = elem ); + } + } + } + + if ( seed ) { + if ( postFinder || preFilter ) { + if ( postFinder ) { + + // Get the final matcherOut by condensing this intermediate into postFinder contexts + temp = []; + i = matcherOut.length; + while ( i-- ) { + if ( ( elem = matcherOut[ i ] ) ) { + + // Restore matcherIn since elem is not yet a final match + temp.push( ( matcherIn[ i ] = elem ) ); + } + } + postFinder( null, ( matcherOut = [] ), temp, xml ); + } + + // Move matched elements from seed to results to keep them synchronized + i = matcherOut.length; + while ( i-- ) { + if ( ( elem = matcherOut[ i ] ) && + ( temp = postFinder ? indexOf( seed, elem ) : preMap[ i ] ) > -1 ) { + + seed[ temp ] = !( results[ temp ] = elem ); + } + } + } + + // Add elements to results, through postFinder if defined + } else { + matcherOut = condense( + matcherOut === results ? + matcherOut.splice( preexisting, matcherOut.length ) : + matcherOut + ); + if ( postFinder ) { + postFinder( null, results, matcherOut, xml ); + } else { + push.apply( results, matcherOut ); + } + } + } ); +} + +function matcherFromTokens( tokens ) { + var checkContext, matcher, j, + len = tokens.length, + leadingRelative = Expr.relative[ tokens[ 0 ].type ], + implicitRelative = leadingRelative || Expr.relative[ " " ], + i = leadingRelative ? 1 : 0, + + // The foundational matcher ensures that elements are reachable from top-level context(s) + matchContext = addCombinator( function( elem ) { + return elem === checkContext; + }, implicitRelative, true ), + matchAnyContext = addCombinator( function( elem ) { + return indexOf( checkContext, elem ) > -1; + }, implicitRelative, true ), + matchers = [ function( elem, context, xml ) { + var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( + ( checkContext = context ).nodeType ? + matchContext( elem, context, xml ) : + matchAnyContext( elem, context, xml ) ); + + // Avoid hanging onto element (issue #299) + checkContext = null; + return ret; + } ]; + + for ( ; i < len; i++ ) { + if ( ( matcher = Expr.relative[ tokens[ i ].type ] ) ) { + matchers = [ addCombinator( elementMatcher( matchers ), matcher ) ]; + } else { + matcher = Expr.filter[ tokens[ i ].type ].apply( null, tokens[ i ].matches ); + + // Return special upon seeing a positional matcher + if ( matcher[ expando ] ) { + + // Find the next relative operator (if any) for proper handling + j = ++i; + for ( ; j < len; j++ ) { + if ( Expr.relative[ tokens[ j ].type ] ) { + break; + } + } + return setMatcher( + i > 1 && elementMatcher( matchers ), + i > 1 && toSelector( + + // If the preceding token was a descendant combinator, insert an implicit any-element `*` + tokens + .slice( 0, i - 1 ) + .concat( { value: tokens[ i - 2 ].type === " " ? "*" : "" } ) + ).replace( rtrim, "$1" ), + matcher, + i < j && matcherFromTokens( tokens.slice( i, j ) ), + j < len && matcherFromTokens( ( tokens = tokens.slice( j ) ) ), + j < len && toSelector( tokens ) + ); + } + matchers.push( matcher ); + } + } + + return elementMatcher( matchers ); +} + +function matcherFromGroupMatchers( elementMatchers, setMatchers ) { + var bySet = setMatchers.length > 0, + byElement = elementMatchers.length > 0, + superMatcher = function( seed, context, xml, results, outermost ) { + var elem, j, matcher, + matchedCount = 0, + i = "0", + unmatched = seed && [], + setMatched = [], + contextBackup = outermostContext, + + // We must always have either seed elements or outermost context + elems = seed || byElement && Expr.find[ "TAG" ]( "*", outermost ), + + // Use integer dirruns iff this is the outermost matcher + dirrunsUnique = ( dirruns += contextBackup == null ? 1 : Math.random() || 0.1 ), + len = elems.length; + + if ( outermost ) { + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + outermostContext = context == document || context || outermost; + } + + // Add elements passing elementMatchers directly to results + // Support: IE<9, Safari + // Tolerate NodeList properties (IE: "length"; Safari: ) matching elements by id + for ( ; i !== len && ( elem = elems[ i ] ) != null; i++ ) { + if ( byElement && elem ) { + j = 0; + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( !context && elem.ownerDocument != document ) { + setDocument( elem ); + xml = !documentIsHTML; + } + while ( ( matcher = elementMatchers[ j++ ] ) ) { + if ( matcher( elem, context || document, xml ) ) { + results.push( elem ); + break; + } + } + if ( outermost ) { + dirruns = dirrunsUnique; + } + } + + // Track unmatched elements for set filters + if ( bySet ) { + + // They will have gone through all possible matchers + if ( ( elem = !matcher && elem ) ) { + matchedCount--; + } + + // Lengthen the array for every element, matched or not + if ( seed ) { + unmatched.push( elem ); + } + } + } + + // `i` is now the count of elements visited above, and adding it to `matchedCount` + // makes the latter nonnegative. + matchedCount += i; + + // Apply set filters to unmatched elements + // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount` + // equals `i`), unless we didn't visit _any_ elements in the above loop because we have + // no element matchers and no seed. + // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that + // case, which will result in a "00" `matchedCount` that differs from `i` but is also + // numerically zero. + if ( bySet && i !== matchedCount ) { + j = 0; + while ( ( matcher = setMatchers[ j++ ] ) ) { + matcher( unmatched, setMatched, context, xml ); + } + + if ( seed ) { + + // Reintegrate element matches to eliminate the need for sorting + if ( matchedCount > 0 ) { + while ( i-- ) { + if ( !( unmatched[ i ] || setMatched[ i ] ) ) { + setMatched[ i ] = pop.call( results ); + } + } + } + + // Discard index placeholder values to get only actual matches + setMatched = condense( setMatched ); + } + + // Add matches to results + push.apply( results, setMatched ); + + // Seedless set matches succeeding multiple successful matchers stipulate sorting + if ( outermost && !seed && setMatched.length > 0 && + ( matchedCount + setMatchers.length ) > 1 ) { + + Sizzle.uniqueSort( results ); + } + } + + // Override manipulation of globals by nested matchers + if ( outermost ) { + dirruns = dirrunsUnique; + outermostContext = contextBackup; + } + + return unmatched; + }; + + return bySet ? + markFunction( superMatcher ) : + superMatcher; +} + +compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) { + var i, + setMatchers = [], + elementMatchers = [], + cached = compilerCache[ selector + " " ]; + + if ( !cached ) { + + // Generate a function of recursive functions that can be used to check each element + if ( !match ) { + match = tokenize( selector ); + } + i = match.length; + while ( i-- ) { + cached = matcherFromTokens( match[ i ] ); + if ( cached[ expando ] ) { + setMatchers.push( cached ); + } else { + elementMatchers.push( cached ); + } + } + + // Cache the compiled function + cached = compilerCache( + selector, + matcherFromGroupMatchers( elementMatchers, setMatchers ) + ); + + // Save selector and tokenization + cached.selector = selector; + } + return cached; +}; + +/** + * A low-level selection function that works with Sizzle's compiled + * selector functions + * @param {String|Function} selector A selector or a pre-compiled + * selector function built with Sizzle.compile + * @param {Element} context + * @param {Array} [results] + * @param {Array} [seed] A set of elements to match against + */ +select = Sizzle.select = function( selector, context, results, seed ) { + var i, tokens, token, type, find, + compiled = typeof selector === "function" && selector, + match = !seed && tokenize( ( selector = compiled.selector || selector ) ); + + results = results || []; + + // Try to minimize operations if there is only one selector in the list and no seed + // (the latter of which guarantees us context) + if ( match.length === 1 ) { + + // Reduce context if the leading compound selector is an ID + tokens = match[ 0 ] = match[ 0 ].slice( 0 ); + if ( tokens.length > 2 && ( token = tokens[ 0 ] ).type === "ID" && + context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[ 1 ].type ] ) { + + context = ( Expr.find[ "ID" ]( token.matches[ 0 ] + .replace( runescape, funescape ), context ) || [] )[ 0 ]; + if ( !context ) { + return results; + + // Precompiled matchers will still verify ancestry, so step up a level + } else if ( compiled ) { + context = context.parentNode; + } + + selector = selector.slice( tokens.shift().value.length ); + } + + // Fetch a seed set for right-to-left matching + i = matchExpr[ "needsContext" ].test( selector ) ? 0 : tokens.length; + while ( i-- ) { + token = tokens[ i ]; + + // Abort if we hit a combinator + if ( Expr.relative[ ( type = token.type ) ] ) { + break; + } + if ( ( find = Expr.find[ type ] ) ) { + + // Search, expanding context for leading sibling combinators + if ( ( seed = find( + token.matches[ 0 ].replace( runescape, funescape ), + rsibling.test( tokens[ 0 ].type ) && testContext( context.parentNode ) || + context + ) ) ) { + + // If seed is empty or no tokens remain, we can return early + tokens.splice( i, 1 ); + selector = seed.length && toSelector( tokens ); + if ( !selector ) { + push.apply( results, seed ); + return results; + } + + break; + } + } + } + } + + // Compile and execute a filtering function if one is not provided + // Provide `match` to avoid retokenization if we modified the selector above + ( compiled || compile( selector, match ) )( + seed, + context, + !documentIsHTML, + results, + !context || rsibling.test( selector ) && testContext( context.parentNode ) || context + ); + return results; +}; + +// One-time assignments + +// Sort stability +support.sortStable = expando.split( "" ).sort( sortOrder ).join( "" ) === expando; + +// Support: Chrome 14-35+ +// Always assume duplicates if they aren't passed to the comparison function +support.detectDuplicates = !!hasDuplicate; + +// Initialize against the default document +setDocument(); + +// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27) +// Detached nodes confoundingly follow *each other* +support.sortDetached = assert( function( el ) { + + // Should return 1, but returns 4 (following) + return el.compareDocumentPosition( document.createElement( "fieldset" ) ) & 1; +} ); + +// Support: IE<8 +// Prevent attribute/property "interpolation" +// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx +if ( !assert( function( el ) { + el.innerHTML = ""; + return el.firstChild.getAttribute( "href" ) === "#"; +} ) ) { + addHandle( "type|href|height|width", function( elem, name, isXML ) { + if ( !isXML ) { + return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 ); + } + } ); +} + +// Support: IE<9 +// Use defaultValue in place of getAttribute("value") +if ( !support.attributes || !assert( function( el ) { + el.innerHTML = ""; + el.firstChild.setAttribute( "value", "" ); + return el.firstChild.getAttribute( "value" ) === ""; +} ) ) { + addHandle( "value", function( elem, _name, isXML ) { + if ( !isXML && elem.nodeName.toLowerCase() === "input" ) { + return elem.defaultValue; + } + } ); +} + +// Support: IE<9 +// Use getAttributeNode to fetch booleans when getAttribute lies +if ( !assert( function( el ) { + return el.getAttribute( "disabled" ) == null; +} ) ) { + addHandle( booleans, function( elem, name, isXML ) { + var val; + if ( !isXML ) { + return elem[ name ] === true ? name.toLowerCase() : + ( val = elem.getAttributeNode( name ) ) && val.specified ? + val.value : + null; + } + } ); +} + +return Sizzle; + +} )( window ); + + + +jQuery.find = Sizzle; +jQuery.expr = Sizzle.selectors; + +// Deprecated +jQuery.expr[ ":" ] = jQuery.expr.pseudos; +jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort; +jQuery.text = Sizzle.getText; +jQuery.isXMLDoc = Sizzle.isXML; +jQuery.contains = Sizzle.contains; +jQuery.escapeSelector = Sizzle.escape; + + + + +var dir = function( elem, dir, until ) { + var matched = [], + truncate = until !== undefined; + + while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) { + if ( elem.nodeType === 1 ) { + if ( truncate && jQuery( elem ).is( until ) ) { + break; + } + matched.push( elem ); + } + } + return matched; +}; + + +var siblings = function( n, elem ) { + var matched = []; + + for ( ; n; n = n.nextSibling ) { + if ( n.nodeType === 1 && n !== elem ) { + matched.push( n ); + } + } + + return matched; +}; + + +var rneedsContext = jQuery.expr.match.needsContext; + + + +function nodeName( elem, name ) { + + return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); + +} +var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i ); + + + +// Implement the identical functionality for filter and not +function winnow( elements, qualifier, not ) { + if ( isFunction( qualifier ) ) { + return jQuery.grep( elements, function( elem, i ) { + return !!qualifier.call( elem, i, elem ) !== not; + } ); + } + + // Single element + if ( qualifier.nodeType ) { + return jQuery.grep( elements, function( elem ) { + return ( elem === qualifier ) !== not; + } ); + } + + // Arraylike of elements (jQuery, arguments, Array) + if ( typeof qualifier !== "string" ) { + return jQuery.grep( elements, function( elem ) { + return ( indexOf.call( qualifier, elem ) > -1 ) !== not; + } ); + } + + // Filtered directly for both simple and complex selectors + return jQuery.filter( qualifier, elements, not ); +} + +jQuery.filter = function( expr, elems, not ) { + var elem = elems[ 0 ]; + + if ( not ) { + expr = ":not(" + expr + ")"; + } + + if ( elems.length === 1 && elem.nodeType === 1 ) { + return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : []; + } + + return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) { + return elem.nodeType === 1; + } ) ); +}; + +jQuery.fn.extend( { + find: function( selector ) { + var i, ret, + len = this.length, + self = this; + + if ( typeof selector !== "string" ) { + return this.pushStack( jQuery( selector ).filter( function() { + for ( i = 0; i < len; i++ ) { + if ( jQuery.contains( self[ i ], this ) ) { + return true; + } + } + } ) ); + } + + ret = this.pushStack( [] ); + + for ( i = 0; i < len; i++ ) { + jQuery.find( selector, self[ i ], ret ); + } + + return len > 1 ? jQuery.uniqueSort( ret ) : ret; + }, + filter: function( selector ) { + return this.pushStack( winnow( this, selector || [], false ) ); + }, + not: function( selector ) { + return this.pushStack( winnow( this, selector || [], true ) ); + }, + is: function( selector ) { + return !!winnow( + this, + + // If this is a positional/relative selector, check membership in the returned set + // so $("p:first").is("p:last") won't return true for a doc with two "p". + typeof selector === "string" && rneedsContext.test( selector ) ? + jQuery( selector ) : + selector || [], + false + ).length; + } +} ); + + +// Initialize a jQuery object + + +// A central reference to the root jQuery(document) +var rootjQuery, + + // A simple way to check for HTML strings + // Prioritize #id over to avoid XSS via location.hash (#9521) + // Strict HTML recognition (#11290: must start with <) + // Shortcut simple #id case for speed + rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/, + + init = jQuery.fn.init = function( selector, context, root ) { + var match, elem; + + // HANDLE: $(""), $(null), $(undefined), $(false) + if ( !selector ) { + return this; + } + + // Method init() accepts an alternate rootjQuery + // so migrate can support jQuery.sub (gh-2101) + root = root || rootjQuery; + + // Handle HTML strings + if ( typeof selector === "string" ) { + if ( selector[ 0 ] === "<" && + selector[ selector.length - 1 ] === ">" && + selector.length >= 3 ) { + + // Assume that strings that start and end with <> are HTML and skip the regex check + match = [ null, selector, null ]; + + } else { + match = rquickExpr.exec( selector ); + } + + // Match html or make sure no context is specified for #id + if ( match && ( match[ 1 ] || !context ) ) { + + // HANDLE: $(html) -> $(array) + if ( match[ 1 ] ) { + context = context instanceof jQuery ? context[ 0 ] : context; + + // Option to run scripts is true for back-compat + // Intentionally let the error be thrown if parseHTML is not present + jQuery.merge( this, jQuery.parseHTML( + match[ 1 ], + context && context.nodeType ? context.ownerDocument || context : document, + true + ) ); + + // HANDLE: $(html, props) + if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) { + for ( match in context ) { + + // Properties of context are called as methods if possible + if ( isFunction( this[ match ] ) ) { + this[ match ]( context[ match ] ); + + // ...and otherwise set as attributes + } else { + this.attr( match, context[ match ] ); + } + } + } + + return this; + + // HANDLE: $(#id) + } else { + elem = document.getElementById( match[ 2 ] ); + + if ( elem ) { + + // Inject the element directly into the jQuery object + this[ 0 ] = elem; + this.length = 1; + } + return this; + } + + // HANDLE: $(expr, $(...)) + } else if ( !context || context.jquery ) { + return ( context || root ).find( selector ); + + // HANDLE: $(expr, context) + // (which is just equivalent to: $(context).find(expr) + } else { + return this.constructor( context ).find( selector ); + } + + // HANDLE: $(DOMElement) + } else if ( selector.nodeType ) { + this[ 0 ] = selector; + this.length = 1; + return this; + + // HANDLE: $(function) + // Shortcut for document ready + } else if ( isFunction( selector ) ) { + return root.ready !== undefined ? + root.ready( selector ) : + + // Execute immediately if ready is not present + selector( jQuery ); + } + + return jQuery.makeArray( selector, this ); + }; + +// Give the init function the jQuery prototype for later instantiation +init.prototype = jQuery.fn; + +// Initialize central reference +rootjQuery = jQuery( document ); + + +var rparentsprev = /^(?:parents|prev(?:Until|All))/, + + // Methods guaranteed to produce a unique set when starting from a unique set + guaranteedUnique = { + children: true, + contents: true, + next: true, + prev: true + }; + +jQuery.fn.extend( { + has: function( target ) { + var targets = jQuery( target, this ), + l = targets.length; + + return this.filter( function() { + var i = 0; + for ( ; i < l; i++ ) { + if ( jQuery.contains( this, targets[ i ] ) ) { + return true; + } + } + } ); + }, + + closest: function( selectors, context ) { + var cur, + i = 0, + l = this.length, + matched = [], + targets = typeof selectors !== "string" && jQuery( selectors ); + + // Positional selectors never match, since there's no _selection_ context + if ( !rneedsContext.test( selectors ) ) { + for ( ; i < l; i++ ) { + for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) { + + // Always skip document fragments + if ( cur.nodeType < 11 && ( targets ? + targets.index( cur ) > -1 : + + // Don't pass non-elements to Sizzle + cur.nodeType === 1 && + jQuery.find.matchesSelector( cur, selectors ) ) ) { + + matched.push( cur ); + break; + } + } + } + } + + return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched ); + }, + + // Determine the position of an element within the set + index: function( elem ) { + + // No argument, return index in parent + if ( !elem ) { + return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1; + } + + // Index in selector + if ( typeof elem === "string" ) { + return indexOf.call( jQuery( elem ), this[ 0 ] ); + } + + // Locate the position of the desired element + return indexOf.call( this, + + // If it receives a jQuery object, the first element is used + elem.jquery ? elem[ 0 ] : elem + ); + }, + + add: function( selector, context ) { + return this.pushStack( + jQuery.uniqueSort( + jQuery.merge( this.get(), jQuery( selector, context ) ) + ) + ); + }, + + addBack: function( selector ) { + return this.add( selector == null ? + this.prevObject : this.prevObject.filter( selector ) + ); + } +} ); + +function sibling( cur, dir ) { + while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {} + return cur; +} + +jQuery.each( { + parent: function( elem ) { + var parent = elem.parentNode; + return parent && parent.nodeType !== 11 ? parent : null; + }, + parents: function( elem ) { + return dir( elem, "parentNode" ); + }, + parentsUntil: function( elem, _i, until ) { + return dir( elem, "parentNode", until ); + }, + next: function( elem ) { + return sibling( elem, "nextSibling" ); + }, + prev: function( elem ) { + return sibling( elem, "previousSibling" ); + }, + nextAll: function( elem ) { + return dir( elem, "nextSibling" ); + }, + prevAll: function( elem ) { + return dir( elem, "previousSibling" ); + }, + nextUntil: function( elem, _i, until ) { + return dir( elem, "nextSibling", until ); + }, + prevUntil: function( elem, _i, until ) { + return dir( elem, "previousSibling", until ); + }, + siblings: function( elem ) { + return siblings( ( elem.parentNode || {} ).firstChild, elem ); + }, + children: function( elem ) { + return siblings( elem.firstChild ); + }, + contents: function( elem ) { + if ( elem.contentDocument != null && + + // Support: IE 11+ + // elements with no `data` attribute has an object + // `contentDocument` with a `null` prototype. + getProto( elem.contentDocument ) ) { + + return elem.contentDocument; + } + + // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only + // Treat the template element as a regular one in browsers that + // don't support it. + if ( nodeName( elem, "template" ) ) { + elem = elem.content || elem; + } + + return jQuery.merge( [], elem.childNodes ); + } +}, function( name, fn ) { + jQuery.fn[ name ] = function( until, selector ) { + var matched = jQuery.map( this, fn, until ); + + if ( name.slice( -5 ) !== "Until" ) { + selector = until; + } + + if ( selector && typeof selector === "string" ) { + matched = jQuery.filter( selector, matched ); + } + + if ( this.length > 1 ) { + + // Remove duplicates + if ( !guaranteedUnique[ name ] ) { + jQuery.uniqueSort( matched ); + } + + // Reverse order for parents* and prev-derivatives + if ( rparentsprev.test( name ) ) { + matched.reverse(); + } + } + + return this.pushStack( matched ); + }; +} ); +var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g ); + + + +// Convert String-formatted options into Object-formatted ones +function createOptions( options ) { + var object = {}; + jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) { + object[ flag ] = true; + } ); + return object; +} + +/* + * Create a callback list using the following parameters: + * + * options: an optional list of space-separated options that will change how + * the callback list behaves or a more traditional option object + * + * By default a callback list will act like an event callback list and can be + * "fired" multiple times. + * + * Possible options: + * + * once: will ensure the callback list can only be fired once (like a Deferred) + * + * memory: will keep track of previous values and will call any callback added + * after the list has been fired right away with the latest "memorized" + * values (like a Deferred) + * + * unique: will ensure a callback can only be added once (no duplicate in the list) + * + * stopOnFalse: interrupt callings when a callback returns false + * + */ +jQuery.Callbacks = function( options ) { + + // Convert options from String-formatted to Object-formatted if needed + // (we check in cache first) + options = typeof options === "string" ? + createOptions( options ) : + jQuery.extend( {}, options ); + + var // Flag to know if list is currently firing + firing, + + // Last fire value for non-forgettable lists + memory, + + // Flag to know if list was already fired + fired, + + // Flag to prevent firing + locked, + + // Actual callback list + list = [], + + // Queue of execution data for repeatable lists + queue = [], + + // Index of currently firing callback (modified by add/remove as needed) + firingIndex = -1, + + // Fire callbacks + fire = function() { + + // Enforce single-firing + locked = locked || options.once; + + // Execute callbacks for all pending executions, + // respecting firingIndex overrides and runtime changes + fired = firing = true; + for ( ; queue.length; firingIndex = -1 ) { + memory = queue.shift(); + while ( ++firingIndex < list.length ) { + + // Run callback and check for early termination + if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false && + options.stopOnFalse ) { + + // Jump to end and forget the data so .add doesn't re-fire + firingIndex = list.length; + memory = false; + } + } + } + + // Forget the data if we're done with it + if ( !options.memory ) { + memory = false; + } + + firing = false; + + // Clean up if we're done firing for good + if ( locked ) { + + // Keep an empty list if we have data for future add calls + if ( memory ) { + list = []; + + // Otherwise, this object is spent + } else { + list = ""; + } + } + }, + + // Actual Callbacks object + self = { + + // Add a callback or a collection of callbacks to the list + add: function() { + if ( list ) { + + // If we have memory from a past run, we should fire after adding + if ( memory && !firing ) { + firingIndex = list.length - 1; + queue.push( memory ); + } + + ( function add( args ) { + jQuery.each( args, function( _, arg ) { + if ( isFunction( arg ) ) { + if ( !options.unique || !self.has( arg ) ) { + list.push( arg ); + } + } else if ( arg && arg.length && toType( arg ) !== "string" ) { + + // Inspect recursively + add( arg ); + } + } ); + } )( arguments ); + + if ( memory && !firing ) { + fire(); + } + } + return this; + }, + + // Remove a callback from the list + remove: function() { + jQuery.each( arguments, function( _, arg ) { + var index; + while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) { + list.splice( index, 1 ); + + // Handle firing indexes + if ( index <= firingIndex ) { + firingIndex--; + } + } + } ); + return this; + }, + + // Check if a given callback is in the list. + // If no argument is given, return whether or not list has callbacks attached. + has: function( fn ) { + return fn ? + jQuery.inArray( fn, list ) > -1 : + list.length > 0; + }, + + // Remove all callbacks from the list + empty: function() { + if ( list ) { + list = []; + } + return this; + }, + + // Disable .fire and .add + // Abort any current/pending executions + // Clear all callbacks and values + disable: function() { + locked = queue = []; + list = memory = ""; + return this; + }, + disabled: function() { + return !list; + }, + + // Disable .fire + // Also disable .add unless we have memory (since it would have no effect) + // Abort any pending executions + lock: function() { + locked = queue = []; + if ( !memory && !firing ) { + list = memory = ""; + } + return this; + }, + locked: function() { + return !!locked; + }, + + // Call all callbacks with the given context and arguments + fireWith: function( context, args ) { + if ( !locked ) { + args = args || []; + args = [ context, args.slice ? args.slice() : args ]; + queue.push( args ); + if ( !firing ) { + fire(); + } + } + return this; + }, + + // Call all the callbacks with the given arguments + fire: function() { + self.fireWith( this, arguments ); + return this; + }, + + // To know if the callbacks have already been called at least once + fired: function() { + return !!fired; + } + }; + + return self; +}; + + +function Identity( v ) { + return v; +} +function Thrower( ex ) { + throw ex; +} + +function adoptValue( value, resolve, reject, noValue ) { + var method; + + try { + + // Check for promise aspect first to privilege synchronous behavior + if ( value && isFunction( ( method = value.promise ) ) ) { + method.call( value ).done( resolve ).fail( reject ); + + // Other thenables + } else if ( value && isFunction( ( method = value.then ) ) ) { + method.call( value, resolve, reject ); + + // Other non-thenables + } else { + + // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer: + // * false: [ value ].slice( 0 ) => resolve( value ) + // * true: [ value ].slice( 1 ) => resolve() + resolve.apply( undefined, [ value ].slice( noValue ) ); + } + + // For Promises/A+, convert exceptions into rejections + // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in + // Deferred#then to conditionally suppress rejection. + } catch ( value ) { + + // Support: Android 4.0 only + // Strict mode functions invoked without .call/.apply get global-object context + reject.apply( undefined, [ value ] ); + } +} + +jQuery.extend( { + + Deferred: function( func ) { + var tuples = [ + + // action, add listener, callbacks, + // ... .then handlers, argument index, [final state] + [ "notify", "progress", jQuery.Callbacks( "memory" ), + jQuery.Callbacks( "memory" ), 2 ], + [ "resolve", "done", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 0, "resolved" ], + [ "reject", "fail", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 1, "rejected" ] + ], + state = "pending", + promise = { + state: function() { + return state; + }, + always: function() { + deferred.done( arguments ).fail( arguments ); + return this; + }, + "catch": function( fn ) { + return promise.then( null, fn ); + }, + + // Keep pipe for back-compat + pipe: function( /* fnDone, fnFail, fnProgress */ ) { + var fns = arguments; + + return jQuery.Deferred( function( newDefer ) { + jQuery.each( tuples, function( _i, tuple ) { + + // Map tuples (progress, done, fail) to arguments (done, fail, progress) + var fn = isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ]; + + // deferred.progress(function() { bind to newDefer or newDefer.notify }) + // deferred.done(function() { bind to newDefer or newDefer.resolve }) + // deferred.fail(function() { bind to newDefer or newDefer.reject }) + deferred[ tuple[ 1 ] ]( function() { + var returned = fn && fn.apply( this, arguments ); + if ( returned && isFunction( returned.promise ) ) { + returned.promise() + .progress( newDefer.notify ) + .done( newDefer.resolve ) + .fail( newDefer.reject ); + } else { + newDefer[ tuple[ 0 ] + "With" ]( + this, + fn ? [ returned ] : arguments + ); + } + } ); + } ); + fns = null; + } ).promise(); + }, + then: function( onFulfilled, onRejected, onProgress ) { + var maxDepth = 0; + function resolve( depth, deferred, handler, special ) { + return function() { + var that = this, + args = arguments, + mightThrow = function() { + var returned, then; + + // Support: Promises/A+ section 2.3.3.3.3 + // https://promisesaplus.com/#point-59 + // Ignore double-resolution attempts + if ( depth < maxDepth ) { + return; + } + + returned = handler.apply( that, args ); + + // Support: Promises/A+ section 2.3.1 + // https://promisesaplus.com/#point-48 + if ( returned === deferred.promise() ) { + throw new TypeError( "Thenable self-resolution" ); + } + + // Support: Promises/A+ sections 2.3.3.1, 3.5 + // https://promisesaplus.com/#point-54 + // https://promisesaplus.com/#point-75 + // Retrieve `then` only once + then = returned && + + // Support: Promises/A+ section 2.3.4 + // https://promisesaplus.com/#point-64 + // Only check objects and functions for thenability + ( typeof returned === "object" || + typeof returned === "function" ) && + returned.then; + + // Handle a returned thenable + if ( isFunction( then ) ) { + + // Special processors (notify) just wait for resolution + if ( special ) { + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ) + ); + + // Normal processors (resolve) also hook into progress + } else { + + // ...and disregard older resolution values + maxDepth++; + + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ), + resolve( maxDepth, deferred, Identity, + deferred.notifyWith ) + ); + } + + // Handle all other returned values + } else { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Identity ) { + that = undefined; + args = [ returned ]; + } + + // Process the value(s) + // Default process is resolve + ( special || deferred.resolveWith )( that, args ); + } + }, + + // Only normal processors (resolve) catch and reject exceptions + process = special ? + mightThrow : + function() { + try { + mightThrow(); + } catch ( e ) { + + if ( jQuery.Deferred.exceptionHook ) { + jQuery.Deferred.exceptionHook( e, + process.stackTrace ); + } + + // Support: Promises/A+ section 2.3.3.3.4.1 + // https://promisesaplus.com/#point-61 + // Ignore post-resolution exceptions + if ( depth + 1 >= maxDepth ) { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Thrower ) { + that = undefined; + args = [ e ]; + } + + deferred.rejectWith( that, args ); + } + } + }; + + // Support: Promises/A+ section 2.3.3.3.1 + // https://promisesaplus.com/#point-57 + // Re-resolve promises immediately to dodge false rejection from + // subsequent errors + if ( depth ) { + process(); + } else { + + // Call an optional hook to record the stack, in case of exception + // since it's otherwise lost when execution goes async + if ( jQuery.Deferred.getStackHook ) { + process.stackTrace = jQuery.Deferred.getStackHook(); + } + window.setTimeout( process ); + } + }; + } + + return jQuery.Deferred( function( newDefer ) { + + // progress_handlers.add( ... ) + tuples[ 0 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onProgress ) ? + onProgress : + Identity, + newDefer.notifyWith + ) + ); + + // fulfilled_handlers.add( ... ) + tuples[ 1 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onFulfilled ) ? + onFulfilled : + Identity + ) + ); + + // rejected_handlers.add( ... ) + tuples[ 2 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onRejected ) ? + onRejected : + Thrower + ) + ); + } ).promise(); + }, + + // Get a promise for this deferred + // If obj is provided, the promise aspect is added to the object + promise: function( obj ) { + return obj != null ? jQuery.extend( obj, promise ) : promise; + } + }, + deferred = {}; + + // Add list-specific methods + jQuery.each( tuples, function( i, tuple ) { + var list = tuple[ 2 ], + stateString = tuple[ 5 ]; + + // promise.progress = list.add + // promise.done = list.add + // promise.fail = list.add + promise[ tuple[ 1 ] ] = list.add; + + // Handle state + if ( stateString ) { + list.add( + function() { + + // state = "resolved" (i.e., fulfilled) + // state = "rejected" + state = stateString; + }, + + // rejected_callbacks.disable + // fulfilled_callbacks.disable + tuples[ 3 - i ][ 2 ].disable, + + // rejected_handlers.disable + // fulfilled_handlers.disable + tuples[ 3 - i ][ 3 ].disable, + + // progress_callbacks.lock + tuples[ 0 ][ 2 ].lock, + + // progress_handlers.lock + tuples[ 0 ][ 3 ].lock + ); + } + + // progress_handlers.fire + // fulfilled_handlers.fire + // rejected_handlers.fire + list.add( tuple[ 3 ].fire ); + + // deferred.notify = function() { deferred.notifyWith(...) } + // deferred.resolve = function() { deferred.resolveWith(...) } + // deferred.reject = function() { deferred.rejectWith(...) } + deferred[ tuple[ 0 ] ] = function() { + deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments ); + return this; + }; + + // deferred.notifyWith = list.fireWith + // deferred.resolveWith = list.fireWith + // deferred.rejectWith = list.fireWith + deferred[ tuple[ 0 ] + "With" ] = list.fireWith; + } ); + + // Make the deferred a promise + promise.promise( deferred ); + + // Call given func if any + if ( func ) { + func.call( deferred, deferred ); + } + + // All done! + return deferred; + }, + + // Deferred helper + when: function( singleValue ) { + var + + // count of uncompleted subordinates + remaining = arguments.length, + + // count of unprocessed arguments + i = remaining, + + // subordinate fulfillment data + resolveContexts = Array( i ), + resolveValues = slice.call( arguments ), + + // the primary Deferred + primary = jQuery.Deferred(), + + // subordinate callback factory + updateFunc = function( i ) { + return function( value ) { + resolveContexts[ i ] = this; + resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value; + if ( !( --remaining ) ) { + primary.resolveWith( resolveContexts, resolveValues ); + } + }; + }; + + // Single- and empty arguments are adopted like Promise.resolve + if ( remaining <= 1 ) { + adoptValue( singleValue, primary.done( updateFunc( i ) ).resolve, primary.reject, + !remaining ); + + // Use .then() to unwrap secondary thenables (cf. gh-3000) + if ( primary.state() === "pending" || + isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) { + + return primary.then(); + } + } + + // Multiple arguments are aggregated like Promise.all array elements + while ( i-- ) { + adoptValue( resolveValues[ i ], updateFunc( i ), primary.reject ); + } + + return primary.promise(); + } +} ); + + +// These usually indicate a programmer mistake during development, +// warn about them ASAP rather than swallowing them by default. +var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/; + +jQuery.Deferred.exceptionHook = function( error, stack ) { + + // Support: IE 8 - 9 only + // Console exists when dev tools are open, which can happen at any time + if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) { + window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack ); + } +}; + + + + +jQuery.readyException = function( error ) { + window.setTimeout( function() { + throw error; + } ); +}; + + + + +// The deferred used on DOM ready +var readyList = jQuery.Deferred(); + +jQuery.fn.ready = function( fn ) { + + readyList + .then( fn ) + + // Wrap jQuery.readyException in a function so that the lookup + // happens at the time of error handling instead of callback + // registration. + .catch( function( error ) { + jQuery.readyException( error ); + } ); + + return this; +}; + +jQuery.extend( { + + // Is the DOM ready to be used? Set to true once it occurs. + isReady: false, + + // A counter to track how many items to wait for before + // the ready event fires. See #6781 + readyWait: 1, + + // Handle when the DOM is ready + ready: function( wait ) { + + // Abort if there are pending holds or we're already ready + if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) { + return; + } + + // Remember that the DOM is ready + jQuery.isReady = true; + + // If a normal DOM Ready event fired, decrement, and wait if need be + if ( wait !== true && --jQuery.readyWait > 0 ) { + return; + } + + // If there are functions bound, to execute + readyList.resolveWith( document, [ jQuery ] ); + } +} ); + +jQuery.ready.then = readyList.then; + +// The ready event handler and self cleanup method +function completed() { + document.removeEventListener( "DOMContentLoaded", completed ); + window.removeEventListener( "load", completed ); + jQuery.ready(); +} + +// Catch cases where $(document).ready() is called +// after the browser event has already occurred. +// Support: IE <=9 - 10 only +// Older IE sometimes signals "interactive" too soon +if ( document.readyState === "complete" || + ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) { + + // Handle it asynchronously to allow scripts the opportunity to delay ready + window.setTimeout( jQuery.ready ); + +} else { + + // Use the handy event callback + document.addEventListener( "DOMContentLoaded", completed ); + + // A fallback to window.onload, that will always work + window.addEventListener( "load", completed ); +} + + + + +// Multifunctional method to get and set values of a collection +// The value/s can optionally be executed if it's a function +var access = function( elems, fn, key, value, chainable, emptyGet, raw ) { + var i = 0, + len = elems.length, + bulk = key == null; + + // Sets many values + if ( toType( key ) === "object" ) { + chainable = true; + for ( i in key ) { + access( elems, fn, i, key[ i ], true, emptyGet, raw ); + } + + // Sets one value + } else if ( value !== undefined ) { + chainable = true; + + if ( !isFunction( value ) ) { + raw = true; + } + + if ( bulk ) { + + // Bulk operations run against the entire set + if ( raw ) { + fn.call( elems, value ); + fn = null; + + // ...except when executing function values + } else { + bulk = fn; + fn = function( elem, _key, value ) { + return bulk.call( jQuery( elem ), value ); + }; + } + } + + if ( fn ) { + for ( ; i < len; i++ ) { + fn( + elems[ i ], key, raw ? + value : + value.call( elems[ i ], i, fn( elems[ i ], key ) ) + ); + } + } + } + + if ( chainable ) { + return elems; + } + + // Gets + if ( bulk ) { + return fn.call( elems ); + } + + return len ? fn( elems[ 0 ], key ) : emptyGet; +}; + + +// Matches dashed string for camelizing +var rmsPrefix = /^-ms-/, + rdashAlpha = /-([a-z])/g; + +// Used by camelCase as callback to replace() +function fcamelCase( _all, letter ) { + return letter.toUpperCase(); +} + +// Convert dashed to camelCase; used by the css and data modules +// Support: IE <=9 - 11, Edge 12 - 15 +// Microsoft forgot to hump their vendor prefix (#9572) +function camelCase( string ) { + return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); +} +var acceptData = function( owner ) { + + // Accepts only: + // - Node + // - Node.ELEMENT_NODE + // - Node.DOCUMENT_NODE + // - Object + // - Any + return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType ); +}; + + + + +function Data() { + this.expando = jQuery.expando + Data.uid++; +} + +Data.uid = 1; + +Data.prototype = { + + cache: function( owner ) { + + // Check if the owner object already has a cache + var value = owner[ this.expando ]; + + // If not, create one + if ( !value ) { + value = {}; + + // We can accept data for non-element nodes in modern browsers, + // but we should not, see #8335. + // Always return an empty object. + if ( acceptData( owner ) ) { + + // If it is a node unlikely to be stringify-ed or looped over + // use plain assignment + if ( owner.nodeType ) { + owner[ this.expando ] = value; + + // Otherwise secure it in a non-enumerable property + // configurable must be true to allow the property to be + // deleted when data is removed + } else { + Object.defineProperty( owner, this.expando, { + value: value, + configurable: true + } ); + } + } + } + + return value; + }, + set: function( owner, data, value ) { + var prop, + cache = this.cache( owner ); + + // Handle: [ owner, key, value ] args + // Always use camelCase key (gh-2257) + if ( typeof data === "string" ) { + cache[ camelCase( data ) ] = value; + + // Handle: [ owner, { properties } ] args + } else { + + // Copy the properties one-by-one to the cache object + for ( prop in data ) { + cache[ camelCase( prop ) ] = data[ prop ]; + } + } + return cache; + }, + get: function( owner, key ) { + return key === undefined ? + this.cache( owner ) : + + // Always use camelCase key (gh-2257) + owner[ this.expando ] && owner[ this.expando ][ camelCase( key ) ]; + }, + access: function( owner, key, value ) { + + // In cases where either: + // + // 1. No key was specified + // 2. A string key was specified, but no value provided + // + // Take the "read" path and allow the get method to determine + // which value to return, respectively either: + // + // 1. The entire cache object + // 2. The data stored at the key + // + if ( key === undefined || + ( ( key && typeof key === "string" ) && value === undefined ) ) { + + return this.get( owner, key ); + } + + // When the key is not a string, or both a key and value + // are specified, set or extend (existing objects) with either: + // + // 1. An object of properties + // 2. A key and value + // + this.set( owner, key, value ); + + // Since the "set" path can have two possible entry points + // return the expected data based on which path was taken[*] + return value !== undefined ? value : key; + }, + remove: function( owner, key ) { + var i, + cache = owner[ this.expando ]; + + if ( cache === undefined ) { + return; + } + + if ( key !== undefined ) { + + // Support array or space separated string of keys + if ( Array.isArray( key ) ) { + + // If key is an array of keys... + // We always set camelCase keys, so remove that. + key = key.map( camelCase ); + } else { + key = camelCase( key ); + + // If a key with the spaces exists, use it. + // Otherwise, create an array by matching non-whitespace + key = key in cache ? + [ key ] : + ( key.match( rnothtmlwhite ) || [] ); + } + + i = key.length; + + while ( i-- ) { + delete cache[ key[ i ] ]; + } + } + + // Remove the expando if there's no more data + if ( key === undefined || jQuery.isEmptyObject( cache ) ) { + + // Support: Chrome <=35 - 45 + // Webkit & Blink performance suffers when deleting properties + // from DOM nodes, so set to undefined instead + // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted) + if ( owner.nodeType ) { + owner[ this.expando ] = undefined; + } else { + delete owner[ this.expando ]; + } + } + }, + hasData: function( owner ) { + var cache = owner[ this.expando ]; + return cache !== undefined && !jQuery.isEmptyObject( cache ); + } +}; +var dataPriv = new Data(); + +var dataUser = new Data(); + + + +// Implementation Summary +// +// 1. Enforce API surface and semantic compatibility with 1.9.x branch +// 2. Improve the module's maintainability by reducing the storage +// paths to a single mechanism. +// 3. Use the same single mechanism to support "private" and "user" data. +// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData) +// 5. Avoid exposing implementation details on user objects (eg. expando properties) +// 6. Provide a clear path for implementation upgrade to WeakMap in 2014 + +var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/, + rmultiDash = /[A-Z]/g; + +function getData( data ) { + if ( data === "true" ) { + return true; + } + + if ( data === "false" ) { + return false; + } + + if ( data === "null" ) { + return null; + } + + // Only convert to a number if it doesn't change the string + if ( data === +data + "" ) { + return +data; + } + + if ( rbrace.test( data ) ) { + return JSON.parse( data ); + } + + return data; +} + +function dataAttr( elem, key, data ) { + var name; + + // If nothing was found internally, try to fetch any + // data from the HTML5 data-* attribute + if ( data === undefined && elem.nodeType === 1 ) { + name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase(); + data = elem.getAttribute( name ); + + if ( typeof data === "string" ) { + try { + data = getData( data ); + } catch ( e ) {} + + // Make sure we set the data so it isn't changed later + dataUser.set( elem, key, data ); + } else { + data = undefined; + } + } + return data; +} + +jQuery.extend( { + hasData: function( elem ) { + return dataUser.hasData( elem ) || dataPriv.hasData( elem ); + }, + + data: function( elem, name, data ) { + return dataUser.access( elem, name, data ); + }, + + removeData: function( elem, name ) { + dataUser.remove( elem, name ); + }, + + // TODO: Now that all calls to _data and _removeData have been replaced + // with direct calls to dataPriv methods, these can be deprecated. + _data: function( elem, name, data ) { + return dataPriv.access( elem, name, data ); + }, + + _removeData: function( elem, name ) { + dataPriv.remove( elem, name ); + } +} ); + +jQuery.fn.extend( { + data: function( key, value ) { + var i, name, data, + elem = this[ 0 ], + attrs = elem && elem.attributes; + + // Gets all values + if ( key === undefined ) { + if ( this.length ) { + data = dataUser.get( elem ); + + if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) { + i = attrs.length; + while ( i-- ) { + + // Support: IE 11 only + // The attrs elements can be null (#14894) + if ( attrs[ i ] ) { + name = attrs[ i ].name; + if ( name.indexOf( "data-" ) === 0 ) { + name = camelCase( name.slice( 5 ) ); + dataAttr( elem, name, data[ name ] ); + } + } + } + dataPriv.set( elem, "hasDataAttrs", true ); + } + } + + return data; + } + + // Sets multiple values + if ( typeof key === "object" ) { + return this.each( function() { + dataUser.set( this, key ); + } ); + } + + return access( this, function( value ) { + var data; + + // The calling jQuery object (element matches) is not empty + // (and therefore has an element appears at this[ 0 ]) and the + // `value` parameter was not undefined. An empty jQuery object + // will result in `undefined` for elem = this[ 0 ] which will + // throw an exception if an attempt to read a data cache is made. + if ( elem && value === undefined ) { + + // Attempt to get data from the cache + // The key will always be camelCased in Data + data = dataUser.get( elem, key ); + if ( data !== undefined ) { + return data; + } + + // Attempt to "discover" the data in + // HTML5 custom data-* attrs + data = dataAttr( elem, key ); + if ( data !== undefined ) { + return data; + } + + // We tried really hard, but the data doesn't exist. + return; + } + + // Set the data... + this.each( function() { + + // We always store the camelCased key + dataUser.set( this, key, value ); + } ); + }, null, value, arguments.length > 1, null, true ); + }, + + removeData: function( key ) { + return this.each( function() { + dataUser.remove( this, key ); + } ); + } +} ); + + +jQuery.extend( { + queue: function( elem, type, data ) { + var queue; + + if ( elem ) { + type = ( type || "fx" ) + "queue"; + queue = dataPriv.get( elem, type ); + + // Speed up dequeue by getting out quickly if this is just a lookup + if ( data ) { + if ( !queue || Array.isArray( data ) ) { + queue = dataPriv.access( elem, type, jQuery.makeArray( data ) ); + } else { + queue.push( data ); + } + } + return queue || []; + } + }, + + dequeue: function( elem, type ) { + type = type || "fx"; + + var queue = jQuery.queue( elem, type ), + startLength = queue.length, + fn = queue.shift(), + hooks = jQuery._queueHooks( elem, type ), + next = function() { + jQuery.dequeue( elem, type ); + }; + + // If the fx queue is dequeued, always remove the progress sentinel + if ( fn === "inprogress" ) { + fn = queue.shift(); + startLength--; + } + + if ( fn ) { + + // Add a progress sentinel to prevent the fx queue from being + // automatically dequeued + if ( type === "fx" ) { + queue.unshift( "inprogress" ); + } + + // Clear up the last queue stop function + delete hooks.stop; + fn.call( elem, next, hooks ); + } + + if ( !startLength && hooks ) { + hooks.empty.fire(); + } + }, + + // Not public - generate a queueHooks object, or return the current one + _queueHooks: function( elem, type ) { + var key = type + "queueHooks"; + return dataPriv.get( elem, key ) || dataPriv.access( elem, key, { + empty: jQuery.Callbacks( "once memory" ).add( function() { + dataPriv.remove( elem, [ type + "queue", key ] ); + } ) + } ); + } +} ); + +jQuery.fn.extend( { + queue: function( type, data ) { + var setter = 2; + + if ( typeof type !== "string" ) { + data = type; + type = "fx"; + setter--; + } + + if ( arguments.length < setter ) { + return jQuery.queue( this[ 0 ], type ); + } + + return data === undefined ? + this : + this.each( function() { + var queue = jQuery.queue( this, type, data ); + + // Ensure a hooks for this queue + jQuery._queueHooks( this, type ); + + if ( type === "fx" && queue[ 0 ] !== "inprogress" ) { + jQuery.dequeue( this, type ); + } + } ); + }, + dequeue: function( type ) { + return this.each( function() { + jQuery.dequeue( this, type ); + } ); + }, + clearQueue: function( type ) { + return this.queue( type || "fx", [] ); + }, + + // Get a promise resolved when queues of a certain type + // are emptied (fx is the type by default) + promise: function( type, obj ) { + var tmp, + count = 1, + defer = jQuery.Deferred(), + elements = this, + i = this.length, + resolve = function() { + if ( !( --count ) ) { + defer.resolveWith( elements, [ elements ] ); + } + }; + + if ( typeof type !== "string" ) { + obj = type; + type = undefined; + } + type = type || "fx"; + + while ( i-- ) { + tmp = dataPriv.get( elements[ i ], type + "queueHooks" ); + if ( tmp && tmp.empty ) { + count++; + tmp.empty.add( resolve ); + } + } + resolve(); + return defer.promise( obj ); + } +} ); +var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source; + +var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ); + + +var cssExpand = [ "Top", "Right", "Bottom", "Left" ]; + +var documentElement = document.documentElement; + + + + var isAttached = function( elem ) { + return jQuery.contains( elem.ownerDocument, elem ); + }, + composed = { composed: true }; + + // Support: IE 9 - 11+, Edge 12 - 18+, iOS 10.0 - 10.2 only + // Check attachment across shadow DOM boundaries when possible (gh-3504) + // Support: iOS 10.0-10.2 only + // Early iOS 10 versions support `attachShadow` but not `getRootNode`, + // leading to errors. We need to check for `getRootNode`. + if ( documentElement.getRootNode ) { + isAttached = function( elem ) { + return jQuery.contains( elem.ownerDocument, elem ) || + elem.getRootNode( composed ) === elem.ownerDocument; + }; + } +var isHiddenWithinTree = function( elem, el ) { + + // isHiddenWithinTree might be called from jQuery#filter function; + // in that case, element will be second argument + elem = el || elem; + + // Inline style trumps all + return elem.style.display === "none" || + elem.style.display === "" && + + // Otherwise, check computed style + // Support: Firefox <=43 - 45 + // Disconnected elements can have computed display: none, so first confirm that elem is + // in the document. + isAttached( elem ) && + + jQuery.css( elem, "display" ) === "none"; + }; + + + +function adjustCSS( elem, prop, valueParts, tween ) { + var adjusted, scale, + maxIterations = 20, + currentValue = tween ? + function() { + return tween.cur(); + } : + function() { + return jQuery.css( elem, prop, "" ); + }, + initial = currentValue(), + unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ), + + // Starting value computation is required for potential unit mismatches + initialInUnit = elem.nodeType && + ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) && + rcssNum.exec( jQuery.css( elem, prop ) ); + + if ( initialInUnit && initialInUnit[ 3 ] !== unit ) { + + // Support: Firefox <=54 + // Halve the iteration target value to prevent interference from CSS upper bounds (gh-2144) + initial = initial / 2; + + // Trust units reported by jQuery.css + unit = unit || initialInUnit[ 3 ]; + + // Iteratively approximate from a nonzero starting point + initialInUnit = +initial || 1; + + while ( maxIterations-- ) { + + // Evaluate and update our best guess (doubling guesses that zero out). + // Finish if the scale equals or crosses 1 (making the old*new product non-positive). + jQuery.style( elem, prop, initialInUnit + unit ); + if ( ( 1 - scale ) * ( 1 - ( scale = currentValue() / initial || 0.5 ) ) <= 0 ) { + maxIterations = 0; + } + initialInUnit = initialInUnit / scale; + + } + + initialInUnit = initialInUnit * 2; + jQuery.style( elem, prop, initialInUnit + unit ); + + // Make sure we update the tween properties later on + valueParts = valueParts || []; + } + + if ( valueParts ) { + initialInUnit = +initialInUnit || +initial || 0; + + // Apply relative offset (+=/-=) if specified + adjusted = valueParts[ 1 ] ? + initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] : + +valueParts[ 2 ]; + if ( tween ) { + tween.unit = unit; + tween.start = initialInUnit; + tween.end = adjusted; + } + } + return adjusted; +} + + +var defaultDisplayMap = {}; + +function getDefaultDisplay( elem ) { + var temp, + doc = elem.ownerDocument, + nodeName = elem.nodeName, + display = defaultDisplayMap[ nodeName ]; + + if ( display ) { + return display; + } + + temp = doc.body.appendChild( doc.createElement( nodeName ) ); + display = jQuery.css( temp, "display" ); + + temp.parentNode.removeChild( temp ); + + if ( display === "none" ) { + display = "block"; + } + defaultDisplayMap[ nodeName ] = display; + + return display; +} + +function showHide( elements, show ) { + var display, elem, + values = [], + index = 0, + length = elements.length; + + // Determine new display value for elements that need to change + for ( ; index < length; index++ ) { + elem = elements[ index ]; + if ( !elem.style ) { + continue; + } + + display = elem.style.display; + if ( show ) { + + // Since we force visibility upon cascade-hidden elements, an immediate (and slow) + // check is required in this first loop unless we have a nonempty display value (either + // inline or about-to-be-restored) + if ( display === "none" ) { + values[ index ] = dataPriv.get( elem, "display" ) || null; + if ( !values[ index ] ) { + elem.style.display = ""; + } + } + if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) { + values[ index ] = getDefaultDisplay( elem ); + } + } else { + if ( display !== "none" ) { + values[ index ] = "none"; + + // Remember what we're overwriting + dataPriv.set( elem, "display", display ); + } + } + } + + // Set the display of the elements in a second loop to avoid constant reflow + for ( index = 0; index < length; index++ ) { + if ( values[ index ] != null ) { + elements[ index ].style.display = values[ index ]; + } + } + + return elements; +} + +jQuery.fn.extend( { + show: function() { + return showHide( this, true ); + }, + hide: function() { + return showHide( this ); + }, + toggle: function( state ) { + if ( typeof state === "boolean" ) { + return state ? this.show() : this.hide(); + } + + return this.each( function() { + if ( isHiddenWithinTree( this ) ) { + jQuery( this ).show(); + } else { + jQuery( this ).hide(); + } + } ); + } +} ); +var rcheckableType = ( /^(?:checkbox|radio)$/i ); + +var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]*)/i ); + +var rscriptType = ( /^$|^module$|\/(?:java|ecma)script/i ); + + + +( function() { + var fragment = document.createDocumentFragment(), + div = fragment.appendChild( document.createElement( "div" ) ), + input = document.createElement( "input" ); + + // Support: Android 4.0 - 4.3 only + // Check state lost if the name is set (#11217) + // Support: Windows Web Apps (WWA) + // `name` and `type` must use .setAttribute for WWA (#14901) + input.setAttribute( "type", "radio" ); + input.setAttribute( "checked", "checked" ); + input.setAttribute( "name", "t" ); + + div.appendChild( input ); + + // Support: Android <=4.1 only + // Older WebKit doesn't clone checked state correctly in fragments + support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked; + + // Support: IE <=11 only + // Make sure textarea (and checkbox) defaultValue is properly cloned + div.innerHTML = ""; + support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue; + + // Support: IE <=9 only + // IE <=9 replaces "; + support.option = !!div.lastChild; +} )(); + + +// We have to close these tags to support XHTML (#13200) +var wrapMap = { + + // XHTML parsers do not magically insert elements in the + // same way that tag soup parsers do. So we cannot shorten + // this by omitting or other required elements. + thead: [ 1, "", "
    " ], + col: [ 2, "", "
    " ], + tr: [ 2, "", "
    " ], + td: [ 3, "", "
    " ], + + _default: [ 0, "", "" ] +}; + +wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; +wrapMap.th = wrapMap.td; + +// Support: IE <=9 only +if ( !support.option ) { + wrapMap.optgroup = wrapMap.option = [ 1, "" ]; +} + + +function getAll( context, tag ) { + + // Support: IE <=9 - 11 only + // Use typeof to avoid zero-argument method invocation on host objects (#15151) + var ret; + + if ( typeof context.getElementsByTagName !== "undefined" ) { + ret = context.getElementsByTagName( tag || "*" ); + + } else if ( typeof context.querySelectorAll !== "undefined" ) { + ret = context.querySelectorAll( tag || "*" ); + + } else { + ret = []; + } + + if ( tag === undefined || tag && nodeName( context, tag ) ) { + return jQuery.merge( [ context ], ret ); + } + + return ret; +} + + +// Mark scripts as having already been evaluated +function setGlobalEval( elems, refElements ) { + var i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + dataPriv.set( + elems[ i ], + "globalEval", + !refElements || dataPriv.get( refElements[ i ], "globalEval" ) + ); + } +} + + +var rhtml = /<|&#?\w+;/; + +function buildFragment( elems, context, scripts, selection, ignored ) { + var elem, tmp, tag, wrap, attached, j, + fragment = context.createDocumentFragment(), + nodes = [], + i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + elem = elems[ i ]; + + if ( elem || elem === 0 ) { + + // Add nodes directly + if ( toType( elem ) === "object" ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem ); + + // Convert non-html into a text node + } else if ( !rhtml.test( elem ) ) { + nodes.push( context.createTextNode( elem ) ); + + // Convert html into DOM nodes + } else { + tmp = tmp || fragment.appendChild( context.createElement( "div" ) ); + + // Deserialize a standard representation + tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase(); + wrap = wrapMap[ tag ] || wrapMap._default; + tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ]; + + // Descend through wrappers to the right content + j = wrap[ 0 ]; + while ( j-- ) { + tmp = tmp.lastChild; + } + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, tmp.childNodes ); + + // Remember the top-level container + tmp = fragment.firstChild; + + // Ensure the created nodes are orphaned (#12392) + tmp.textContent = ""; + } + } + } + + // Remove wrapper from fragment + fragment.textContent = ""; + + i = 0; + while ( ( elem = nodes[ i++ ] ) ) { + + // Skip elements already in the context collection (trac-4087) + if ( selection && jQuery.inArray( elem, selection ) > -1 ) { + if ( ignored ) { + ignored.push( elem ); + } + continue; + } + + attached = isAttached( elem ); + + // Append to fragment + tmp = getAll( fragment.appendChild( elem ), "script" ); + + // Preserve script evaluation history + if ( attached ) { + setGlobalEval( tmp ); + } + + // Capture executables + if ( scripts ) { + j = 0; + while ( ( elem = tmp[ j++ ] ) ) { + if ( rscriptType.test( elem.type || "" ) ) { + scripts.push( elem ); + } + } + } + } + + return fragment; +} + + +var rtypenamespace = /^([^.]*)(?:\.(.+)|)/; + +function returnTrue() { + return true; +} + +function returnFalse() { + return false; +} + +// Support: IE <=9 - 11+ +// focus() and blur() are asynchronous, except when they are no-op. +// So expect focus to be synchronous when the element is already active, +// and blur to be synchronous when the element is not already active. +// (focus and blur are always synchronous in other supported browsers, +// this just defines when we can count on it). +function expectSync( elem, type ) { + return ( elem === safeActiveElement() ) === ( type === "focus" ); +} + +// Support: IE <=9 only +// Accessing document.activeElement can throw unexpectedly +// https://bugs.jquery.com/ticket/13393 +function safeActiveElement() { + try { + return document.activeElement; + } catch ( err ) { } +} + +function on( elem, types, selector, data, fn, one ) { + var origFn, type; + + // Types can be a map of types/handlers + if ( typeof types === "object" ) { + + // ( types-Object, selector, data ) + if ( typeof selector !== "string" ) { + + // ( types-Object, data ) + data = data || selector; + selector = undefined; + } + for ( type in types ) { + on( elem, type, selector, data, types[ type ], one ); + } + return elem; + } + + if ( data == null && fn == null ) { + + // ( types, fn ) + fn = selector; + data = selector = undefined; + } else if ( fn == null ) { + if ( typeof selector === "string" ) { + + // ( types, selector, fn ) + fn = data; + data = undefined; + } else { + + // ( types, data, fn ) + fn = data; + data = selector; + selector = undefined; + } + } + if ( fn === false ) { + fn = returnFalse; + } else if ( !fn ) { + return elem; + } + + if ( one === 1 ) { + origFn = fn; + fn = function( event ) { + + // Can use an empty set, since event contains the info + jQuery().off( event ); + return origFn.apply( this, arguments ); + }; + + // Use same guid so caller can remove using origFn + fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); + } + return elem.each( function() { + jQuery.event.add( this, types, fn, data, selector ); + } ); +} + +/* + * Helper functions for managing events -- not part of the public interface. + * Props to Dean Edwards' addEvent library for many of the ideas. + */ +jQuery.event = { + + global: {}, + + add: function( elem, types, handler, data, selector ) { + + var handleObjIn, eventHandle, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.get( elem ); + + // Only attach events to objects that accept data + if ( !acceptData( elem ) ) { + return; + } + + // Caller can pass in an object of custom data in lieu of the handler + if ( handler.handler ) { + handleObjIn = handler; + handler = handleObjIn.handler; + selector = handleObjIn.selector; + } + + // Ensure that invalid selectors throw exceptions at attach time + // Evaluate against documentElement in case elem is a non-element node (e.g., document) + if ( selector ) { + jQuery.find.matchesSelector( documentElement, selector ); + } + + // Make sure that the handler has a unique ID, used to find/remove it later + if ( !handler.guid ) { + handler.guid = jQuery.guid++; + } + + // Init the element's event structure and main handler, if this is the first + if ( !( events = elemData.events ) ) { + events = elemData.events = Object.create( null ); + } + if ( !( eventHandle = elemData.handle ) ) { + eventHandle = elemData.handle = function( e ) { + + // Discard the second event of a jQuery.event.trigger() and + // when an event is called after a page has unloaded + return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? + jQuery.event.dispatch.apply( elem, arguments ) : undefined; + }; + } + + // Handle multiple events separated by a space + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // There *must* be a type, no attaching namespace-only handlers + if ( !type ) { + continue; + } + + // If event changes its type, use the special event handlers for the changed type + special = jQuery.event.special[ type ] || {}; + + // If selector defined, determine special event api type, otherwise given type + type = ( selector ? special.delegateType : special.bindType ) || type; + + // Update special based on newly reset type + special = jQuery.event.special[ type ] || {}; + + // handleObj is passed to all event handlers + handleObj = jQuery.extend( { + type: type, + origType: origType, + data: data, + handler: handler, + guid: handler.guid, + selector: selector, + needsContext: selector && jQuery.expr.match.needsContext.test( selector ), + namespace: namespaces.join( "." ) + }, handleObjIn ); + + // Init the event handler queue if we're the first + if ( !( handlers = events[ type ] ) ) { + handlers = events[ type ] = []; + handlers.delegateCount = 0; + + // Only use addEventListener if the special events handler returns false + if ( !special.setup || + special.setup.call( elem, data, namespaces, eventHandle ) === false ) { + + if ( elem.addEventListener ) { + elem.addEventListener( type, eventHandle ); + } + } + } + + if ( special.add ) { + special.add.call( elem, handleObj ); + + if ( !handleObj.handler.guid ) { + handleObj.handler.guid = handler.guid; + } + } + + // Add to the element's handler list, delegates in front + if ( selector ) { + handlers.splice( handlers.delegateCount++, 0, handleObj ); + } else { + handlers.push( handleObj ); + } + + // Keep track of which events have ever been used, for event optimization + jQuery.event.global[ type ] = true; + } + + }, + + // Detach an event or set of events from an element + remove: function( elem, types, handler, selector, mappedTypes ) { + + var j, origCount, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.hasData( elem ) && dataPriv.get( elem ); + + if ( !elemData || !( events = elemData.events ) ) { + return; + } + + // Once for each type.namespace in types; type may be omitted + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // Unbind all events (on this namespace, if provided) for the element + if ( !type ) { + for ( type in events ) { + jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); + } + continue; + } + + special = jQuery.event.special[ type ] || {}; + type = ( selector ? special.delegateType : special.bindType ) || type; + handlers = events[ type ] || []; + tmp = tmp[ 2 ] && + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ); + + // Remove matching events + origCount = j = handlers.length; + while ( j-- ) { + handleObj = handlers[ j ]; + + if ( ( mappedTypes || origType === handleObj.origType ) && + ( !handler || handler.guid === handleObj.guid ) && + ( !tmp || tmp.test( handleObj.namespace ) ) && + ( !selector || selector === handleObj.selector || + selector === "**" && handleObj.selector ) ) { + handlers.splice( j, 1 ); + + if ( handleObj.selector ) { + handlers.delegateCount--; + } + if ( special.remove ) { + special.remove.call( elem, handleObj ); + } + } + } + + // Remove generic event handler if we removed something and no more handlers exist + // (avoids potential for endless recursion during removal of special event handlers) + if ( origCount && !handlers.length ) { + if ( !special.teardown || + special.teardown.call( elem, namespaces, elemData.handle ) === false ) { + + jQuery.removeEvent( elem, type, elemData.handle ); + } + + delete events[ type ]; + } + } + + // Remove data and the expando if it's no longer used + if ( jQuery.isEmptyObject( events ) ) { + dataPriv.remove( elem, "handle events" ); + } + }, + + dispatch: function( nativeEvent ) { + + var i, j, ret, matched, handleObj, handlerQueue, + args = new Array( arguments.length ), + + // Make a writable jQuery.Event from the native event object + event = jQuery.event.fix( nativeEvent ), + + handlers = ( + dataPriv.get( this, "events" ) || Object.create( null ) + )[ event.type ] || [], + special = jQuery.event.special[ event.type ] || {}; + + // Use the fix-ed jQuery.Event rather than the (read-only) native event + args[ 0 ] = event; + + for ( i = 1; i < arguments.length; i++ ) { + args[ i ] = arguments[ i ]; + } + + event.delegateTarget = this; + + // Call the preDispatch hook for the mapped type, and let it bail if desired + if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { + return; + } + + // Determine handlers + handlerQueue = jQuery.event.handlers.call( this, event, handlers ); + + // Run delegates first; they may want to stop propagation beneath us + i = 0; + while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) { + event.currentTarget = matched.elem; + + j = 0; + while ( ( handleObj = matched.handlers[ j++ ] ) && + !event.isImmediatePropagationStopped() ) { + + // If the event is namespaced, then each handler is only invoked if it is + // specially universal or its namespaces are a superset of the event's. + if ( !event.rnamespace || handleObj.namespace === false || + event.rnamespace.test( handleObj.namespace ) ) { + + event.handleObj = handleObj; + event.data = handleObj.data; + + ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle || + handleObj.handler ).apply( matched.elem, args ); + + if ( ret !== undefined ) { + if ( ( event.result = ret ) === false ) { + event.preventDefault(); + event.stopPropagation(); + } + } + } + } + } + + // Call the postDispatch hook for the mapped type + if ( special.postDispatch ) { + special.postDispatch.call( this, event ); + } + + return event.result; + }, + + handlers: function( event, handlers ) { + var i, handleObj, sel, matchedHandlers, matchedSelectors, + handlerQueue = [], + delegateCount = handlers.delegateCount, + cur = event.target; + + // Find delegate handlers + if ( delegateCount && + + // Support: IE <=9 + // Black-hole SVG instance trees (trac-13180) + cur.nodeType && + + // Support: Firefox <=42 + // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861) + // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click + // Support: IE 11 only + // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343) + !( event.type === "click" && event.button >= 1 ) ) { + + for ( ; cur !== this; cur = cur.parentNode || this ) { + + // Don't check non-elements (#13208) + // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) + if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) { + matchedHandlers = []; + matchedSelectors = {}; + for ( i = 0; i < delegateCount; i++ ) { + handleObj = handlers[ i ]; + + // Don't conflict with Object.prototype properties (#13203) + sel = handleObj.selector + " "; + + if ( matchedSelectors[ sel ] === undefined ) { + matchedSelectors[ sel ] = handleObj.needsContext ? + jQuery( sel, this ).index( cur ) > -1 : + jQuery.find( sel, this, null, [ cur ] ).length; + } + if ( matchedSelectors[ sel ] ) { + matchedHandlers.push( handleObj ); + } + } + if ( matchedHandlers.length ) { + handlerQueue.push( { elem: cur, handlers: matchedHandlers } ); + } + } + } + } + + // Add the remaining (directly-bound) handlers + cur = this; + if ( delegateCount < handlers.length ) { + handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } ); + } + + return handlerQueue; + }, + + addProp: function( name, hook ) { + Object.defineProperty( jQuery.Event.prototype, name, { + enumerable: true, + configurable: true, + + get: isFunction( hook ) ? + function() { + if ( this.originalEvent ) { + return hook( this.originalEvent ); + } + } : + function() { + if ( this.originalEvent ) { + return this.originalEvent[ name ]; + } + }, + + set: function( value ) { + Object.defineProperty( this, name, { + enumerable: true, + configurable: true, + writable: true, + value: value + } ); + } + } ); + }, + + fix: function( originalEvent ) { + return originalEvent[ jQuery.expando ] ? + originalEvent : + new jQuery.Event( originalEvent ); + }, + + special: { + load: { + + // Prevent triggered image.load events from bubbling to window.load + noBubble: true + }, + click: { + + // Utilize native event to ensure correct state for checkable inputs + setup: function( data ) { + + // For mutual compressibility with _default, replace `this` access with a local var. + // `|| data` is dead code meant only to preserve the variable through minification. + var el = this || data; + + // Claim the first handler + if ( rcheckableType.test( el.type ) && + el.click && nodeName( el, "input" ) ) { + + // dataPriv.set( el, "click", ... ) + leverageNative( el, "click", returnTrue ); + } + + // Return false to allow normal processing in the caller + return false; + }, + trigger: function( data ) { + + // For mutual compressibility with _default, replace `this` access with a local var. + // `|| data` is dead code meant only to preserve the variable through minification. + var el = this || data; + + // Force setup before triggering a click + if ( rcheckableType.test( el.type ) && + el.click && nodeName( el, "input" ) ) { + + leverageNative( el, "click" ); + } + + // Return non-false to allow normal event-path propagation + return true; + }, + + // For cross-browser consistency, suppress native .click() on links + // Also prevent it if we're currently inside a leveraged native-event stack + _default: function( event ) { + var target = event.target; + return rcheckableType.test( target.type ) && + target.click && nodeName( target, "input" ) && + dataPriv.get( target, "click" ) || + nodeName( target, "a" ); + } + }, + + beforeunload: { + postDispatch: function( event ) { + + // Support: Firefox 20+ + // Firefox doesn't alert if the returnValue field is not set. + if ( event.result !== undefined && event.originalEvent ) { + event.originalEvent.returnValue = event.result; + } + } + } + } +}; + +// Ensure the presence of an event listener that handles manually-triggered +// synthetic events by interrupting progress until reinvoked in response to +// *native* events that it fires directly, ensuring that state changes have +// already occurred before other listeners are invoked. +function leverageNative( el, type, expectSync ) { + + // Missing expectSync indicates a trigger call, which must force setup through jQuery.event.add + if ( !expectSync ) { + if ( dataPriv.get( el, type ) === undefined ) { + jQuery.event.add( el, type, returnTrue ); + } + return; + } + + // Register the controller as a special universal handler for all event namespaces + dataPriv.set( el, type, false ); + jQuery.event.add( el, type, { + namespace: false, + handler: function( event ) { + var notAsync, result, + saved = dataPriv.get( this, type ); + + if ( ( event.isTrigger & 1 ) && this[ type ] ) { + + // Interrupt processing of the outer synthetic .trigger()ed event + // Saved data should be false in such cases, but might be a leftover capture object + // from an async native handler (gh-4350) + if ( !saved.length ) { + + // Store arguments for use when handling the inner native event + // There will always be at least one argument (an event object), so this array + // will not be confused with a leftover capture object. + saved = slice.call( arguments ); + dataPriv.set( this, type, saved ); + + // Trigger the native event and capture its result + // Support: IE <=9 - 11+ + // focus() and blur() are asynchronous + notAsync = expectSync( this, type ); + this[ type ](); + result = dataPriv.get( this, type ); + if ( saved !== result || notAsync ) { + dataPriv.set( this, type, false ); + } else { + result = {}; + } + if ( saved !== result ) { + + // Cancel the outer synthetic event + event.stopImmediatePropagation(); + event.preventDefault(); + + // Support: Chrome 86+ + // In Chrome, if an element having a focusout handler is blurred by + // clicking outside of it, it invokes the handler synchronously. If + // that handler calls `.remove()` on the element, the data is cleared, + // leaving `result` undefined. We need to guard against this. + return result && result.value; + } + + // If this is an inner synthetic event for an event with a bubbling surrogate + // (focus or blur), assume that the surrogate already propagated from triggering the + // native event and prevent that from happening again here. + // This technically gets the ordering wrong w.r.t. to `.trigger()` (in which the + // bubbling surrogate propagates *after* the non-bubbling base), but that seems + // less bad than duplication. + } else if ( ( jQuery.event.special[ type ] || {} ).delegateType ) { + event.stopPropagation(); + } + + // If this is a native event triggered above, everything is now in order + // Fire an inner synthetic event with the original arguments + } else if ( saved.length ) { + + // ...and capture the result + dataPriv.set( this, type, { + value: jQuery.event.trigger( + + // Support: IE <=9 - 11+ + // Extend with the prototype to reset the above stopImmediatePropagation() + jQuery.extend( saved[ 0 ], jQuery.Event.prototype ), + saved.slice( 1 ), + this + ) + } ); + + // Abort handling of the native event + event.stopImmediatePropagation(); + } + } + } ); +} + +jQuery.removeEvent = function( elem, type, handle ) { + + // This "if" is needed for plain objects + if ( elem.removeEventListener ) { + elem.removeEventListener( type, handle ); + } +}; + +jQuery.Event = function( src, props ) { + + // Allow instantiation without the 'new' keyword + if ( !( this instanceof jQuery.Event ) ) { + return new jQuery.Event( src, props ); + } + + // Event object + if ( src && src.type ) { + this.originalEvent = src; + this.type = src.type; + + // Events bubbling up the document may have been marked as prevented + // by a handler lower down the tree; reflect the correct value. + this.isDefaultPrevented = src.defaultPrevented || + src.defaultPrevented === undefined && + + // Support: Android <=2.3 only + src.returnValue === false ? + returnTrue : + returnFalse; + + // Create target properties + // Support: Safari <=6 - 7 only + // Target should not be a text node (#504, #13143) + this.target = ( src.target && src.target.nodeType === 3 ) ? + src.target.parentNode : + src.target; + + this.currentTarget = src.currentTarget; + this.relatedTarget = src.relatedTarget; + + // Event type + } else { + this.type = src; + } + + // Put explicitly provided properties onto the event object + if ( props ) { + jQuery.extend( this, props ); + } + + // Create a timestamp if incoming event doesn't have one + this.timeStamp = src && src.timeStamp || Date.now(); + + // Mark it as fixed + this[ jQuery.expando ] = true; +}; + +// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding +// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html +jQuery.Event.prototype = { + constructor: jQuery.Event, + isDefaultPrevented: returnFalse, + isPropagationStopped: returnFalse, + isImmediatePropagationStopped: returnFalse, + isSimulated: false, + + preventDefault: function() { + var e = this.originalEvent; + + this.isDefaultPrevented = returnTrue; + + if ( e && !this.isSimulated ) { + e.preventDefault(); + } + }, + stopPropagation: function() { + var e = this.originalEvent; + + this.isPropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopPropagation(); + } + }, + stopImmediatePropagation: function() { + var e = this.originalEvent; + + this.isImmediatePropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopImmediatePropagation(); + } + + this.stopPropagation(); + } +}; + +// Includes all common event props including KeyEvent and MouseEvent specific props +jQuery.each( { + altKey: true, + bubbles: true, + cancelable: true, + changedTouches: true, + ctrlKey: true, + detail: true, + eventPhase: true, + metaKey: true, + pageX: true, + pageY: true, + shiftKey: true, + view: true, + "char": true, + code: true, + charCode: true, + key: true, + keyCode: true, + button: true, + buttons: true, + clientX: true, + clientY: true, + offsetX: true, + offsetY: true, + pointerId: true, + pointerType: true, + screenX: true, + screenY: true, + targetTouches: true, + toElement: true, + touches: true, + which: true +}, jQuery.event.addProp ); + +jQuery.each( { focus: "focusin", blur: "focusout" }, function( type, delegateType ) { + jQuery.event.special[ type ] = { + + // Utilize native event if possible so blur/focus sequence is correct + setup: function() { + + // Claim the first handler + // dataPriv.set( this, "focus", ... ) + // dataPriv.set( this, "blur", ... ) + leverageNative( this, type, expectSync ); + + // Return false to allow normal processing in the caller + return false; + }, + trigger: function() { + + // Force setup before trigger + leverageNative( this, type ); + + // Return non-false to allow normal event-path propagation + return true; + }, + + // Suppress native focus or blur as it's already being fired + // in leverageNative. + _default: function() { + return true; + }, + + delegateType: delegateType + }; +} ); + +// Create mouseenter/leave events using mouseover/out and event-time checks +// so that event delegation works in jQuery. +// Do the same for pointerenter/pointerleave and pointerover/pointerout +// +// Support: Safari 7 only +// Safari sends mouseenter too often; see: +// https://bugs.chromium.org/p/chromium/issues/detail?id=470258 +// for the description of the bug (it existed in older Chrome versions as well). +jQuery.each( { + mouseenter: "mouseover", + mouseleave: "mouseout", + pointerenter: "pointerover", + pointerleave: "pointerout" +}, function( orig, fix ) { + jQuery.event.special[ orig ] = { + delegateType: fix, + bindType: fix, + + handle: function( event ) { + var ret, + target = this, + related = event.relatedTarget, + handleObj = event.handleObj; + + // For mouseenter/leave call the handler if related is outside the target. + // NB: No relatedTarget if the mouse left/entered the browser window + if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) { + event.type = handleObj.origType; + ret = handleObj.handler.apply( this, arguments ); + event.type = fix; + } + return ret; + } + }; +} ); + +jQuery.fn.extend( { + + on: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn ); + }, + one: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn, 1 ); + }, + off: function( types, selector, fn ) { + var handleObj, type; + if ( types && types.preventDefault && types.handleObj ) { + + // ( event ) dispatched jQuery.Event + handleObj = types.handleObj; + jQuery( types.delegateTarget ).off( + handleObj.namespace ? + handleObj.origType + "." + handleObj.namespace : + handleObj.origType, + handleObj.selector, + handleObj.handler + ); + return this; + } + if ( typeof types === "object" ) { + + // ( types-object [, selector] ) + for ( type in types ) { + this.off( type, selector, types[ type ] ); + } + return this; + } + if ( selector === false || typeof selector === "function" ) { + + // ( types [, fn] ) + fn = selector; + selector = undefined; + } + if ( fn === false ) { + fn = returnFalse; + } + return this.each( function() { + jQuery.event.remove( this, types, fn, selector ); + } ); + } +} ); + + +var + + // Support: IE <=10 - 11, Edge 12 - 13 only + // In IE/Edge using regex groups here causes severe slowdowns. + // See https://connect.microsoft.com/IE/feedback/details/1736512/ + rnoInnerhtml = /\s*$/g; + +// Prefer a tbody over its parent table for containing new rows +function manipulationTarget( elem, content ) { + if ( nodeName( elem, "table" ) && + nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) { + + return jQuery( elem ).children( "tbody" )[ 0 ] || elem; + } + + return elem; +} + +// Replace/restore the type attribute of script elements for safe DOM manipulation +function disableScript( elem ) { + elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type; + return elem; +} +function restoreScript( elem ) { + if ( ( elem.type || "" ).slice( 0, 5 ) === "true/" ) { + elem.type = elem.type.slice( 5 ); + } else { + elem.removeAttribute( "type" ); + } + + return elem; +} + +function cloneCopyEvent( src, dest ) { + var i, l, type, pdataOld, udataOld, udataCur, events; + + if ( dest.nodeType !== 1 ) { + return; + } + + // 1. Copy private data: events, handlers, etc. + if ( dataPriv.hasData( src ) ) { + pdataOld = dataPriv.get( src ); + events = pdataOld.events; + + if ( events ) { + dataPriv.remove( dest, "handle events" ); + + for ( type in events ) { + for ( i = 0, l = events[ type ].length; i < l; i++ ) { + jQuery.event.add( dest, type, events[ type ][ i ] ); + } + } + } + } + + // 2. Copy user data + if ( dataUser.hasData( src ) ) { + udataOld = dataUser.access( src ); + udataCur = jQuery.extend( {}, udataOld ); + + dataUser.set( dest, udataCur ); + } +} + +// Fix IE bugs, see support tests +function fixInput( src, dest ) { + var nodeName = dest.nodeName.toLowerCase(); + + // Fails to persist the checked state of a cloned checkbox or radio button. + if ( nodeName === "input" && rcheckableType.test( src.type ) ) { + dest.checked = src.checked; + + // Fails to return the selected option to the default selected state when cloning options + } else if ( nodeName === "input" || nodeName === "textarea" ) { + dest.defaultValue = src.defaultValue; + } +} + +function domManip( collection, args, callback, ignored ) { + + // Flatten any nested arrays + args = flat( args ); + + var fragment, first, scripts, hasScripts, node, doc, + i = 0, + l = collection.length, + iNoClone = l - 1, + value = args[ 0 ], + valueIsFunction = isFunction( value ); + + // We can't cloneNode fragments that contain checked, in WebKit + if ( valueIsFunction || + ( l > 1 && typeof value === "string" && + !support.checkClone && rchecked.test( value ) ) ) { + return collection.each( function( index ) { + var self = collection.eq( index ); + if ( valueIsFunction ) { + args[ 0 ] = value.call( this, index, self.html() ); + } + domManip( self, args, callback, ignored ); + } ); + } + + if ( l ) { + fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored ); + first = fragment.firstChild; + + if ( fragment.childNodes.length === 1 ) { + fragment = first; + } + + // Require either new content or an interest in ignored elements to invoke the callback + if ( first || ignored ) { + scripts = jQuery.map( getAll( fragment, "script" ), disableScript ); + hasScripts = scripts.length; + + // Use the original fragment for the last item + // instead of the first because it can end up + // being emptied incorrectly in certain situations (#8070). + for ( ; i < l; i++ ) { + node = fragment; + + if ( i !== iNoClone ) { + node = jQuery.clone( node, true, true ); + + // Keep references to cloned scripts for later restoration + if ( hasScripts ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( scripts, getAll( node, "script" ) ); + } + } + + callback.call( collection[ i ], node, i ); + } + + if ( hasScripts ) { + doc = scripts[ scripts.length - 1 ].ownerDocument; + + // Reenable scripts + jQuery.map( scripts, restoreScript ); + + // Evaluate executable scripts on first document insertion + for ( i = 0; i < hasScripts; i++ ) { + node = scripts[ i ]; + if ( rscriptType.test( node.type || "" ) && + !dataPriv.access( node, "globalEval" ) && + jQuery.contains( doc, node ) ) { + + if ( node.src && ( node.type || "" ).toLowerCase() !== "module" ) { + + // Optional AJAX dependency, but won't run scripts if not present + if ( jQuery._evalUrl && !node.noModule ) { + jQuery._evalUrl( node.src, { + nonce: node.nonce || node.getAttribute( "nonce" ) + }, doc ); + } + } else { + DOMEval( node.textContent.replace( rcleanScript, "" ), node, doc ); + } + } + } + } + } + } + + return collection; +} + +function remove( elem, selector, keepData ) { + var node, + nodes = selector ? jQuery.filter( selector, elem ) : elem, + i = 0; + + for ( ; ( node = nodes[ i ] ) != null; i++ ) { + if ( !keepData && node.nodeType === 1 ) { + jQuery.cleanData( getAll( node ) ); + } + + if ( node.parentNode ) { + if ( keepData && isAttached( node ) ) { + setGlobalEval( getAll( node, "script" ) ); + } + node.parentNode.removeChild( node ); + } + } + + return elem; +} + +jQuery.extend( { + htmlPrefilter: function( html ) { + return html; + }, + + clone: function( elem, dataAndEvents, deepDataAndEvents ) { + var i, l, srcElements, destElements, + clone = elem.cloneNode( true ), + inPage = isAttached( elem ); + + // Fix IE cloning issues + if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) && + !jQuery.isXMLDoc( elem ) ) { + + // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2 + destElements = getAll( clone ); + srcElements = getAll( elem ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + fixInput( srcElements[ i ], destElements[ i ] ); + } + } + + // Copy the events from the original to the clone + if ( dataAndEvents ) { + if ( deepDataAndEvents ) { + srcElements = srcElements || getAll( elem ); + destElements = destElements || getAll( clone ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + cloneCopyEvent( srcElements[ i ], destElements[ i ] ); + } + } else { + cloneCopyEvent( elem, clone ); + } + } + + // Preserve script evaluation history + destElements = getAll( clone, "script" ); + if ( destElements.length > 0 ) { + setGlobalEval( destElements, !inPage && getAll( elem, "script" ) ); + } + + // Return the cloned set + return clone; + }, + + cleanData: function( elems ) { + var data, elem, type, + special = jQuery.event.special, + i = 0; + + for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) { + if ( acceptData( elem ) ) { + if ( ( data = elem[ dataPriv.expando ] ) ) { + if ( data.events ) { + for ( type in data.events ) { + if ( special[ type ] ) { + jQuery.event.remove( elem, type ); + + // This is a shortcut to avoid jQuery.event.remove's overhead + } else { + jQuery.removeEvent( elem, type, data.handle ); + } + } + } + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataPriv.expando ] = undefined; + } + if ( elem[ dataUser.expando ] ) { + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataUser.expando ] = undefined; + } + } + } + } +} ); + +jQuery.fn.extend( { + detach: function( selector ) { + return remove( this, selector, true ); + }, + + remove: function( selector ) { + return remove( this, selector ); + }, + + text: function( value ) { + return access( this, function( value ) { + return value === undefined ? + jQuery.text( this ) : + this.empty().each( function() { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + this.textContent = value; + } + } ); + }, null, value, arguments.length ); + }, + + append: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.appendChild( elem ); + } + } ); + }, + + prepend: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.insertBefore( elem, target.firstChild ); + } + } ); + }, + + before: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this ); + } + } ); + }, + + after: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this.nextSibling ); + } + } ); + }, + + empty: function() { + var elem, + i = 0; + + for ( ; ( elem = this[ i ] ) != null; i++ ) { + if ( elem.nodeType === 1 ) { + + // Prevent memory leaks + jQuery.cleanData( getAll( elem, false ) ); + + // Remove any remaining nodes + elem.textContent = ""; + } + } + + return this; + }, + + clone: function( dataAndEvents, deepDataAndEvents ) { + dataAndEvents = dataAndEvents == null ? false : dataAndEvents; + deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; + + return this.map( function() { + return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); + } ); + }, + + html: function( value ) { + return access( this, function( value ) { + var elem = this[ 0 ] || {}, + i = 0, + l = this.length; + + if ( value === undefined && elem.nodeType === 1 ) { + return elem.innerHTML; + } + + // See if we can take a shortcut and just use innerHTML + if ( typeof value === "string" && !rnoInnerhtml.test( value ) && + !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) { + + value = jQuery.htmlPrefilter( value ); + + try { + for ( ; i < l; i++ ) { + elem = this[ i ] || {}; + + // Remove element nodes and prevent memory leaks + if ( elem.nodeType === 1 ) { + jQuery.cleanData( getAll( elem, false ) ); + elem.innerHTML = value; + } + } + + elem = 0; + + // If using innerHTML throws an exception, use the fallback method + } catch ( e ) {} + } + + if ( elem ) { + this.empty().append( value ); + } + }, null, value, arguments.length ); + }, + + replaceWith: function() { + var ignored = []; + + // Make the changes, replacing each non-ignored context element with the new content + return domManip( this, arguments, function( elem ) { + var parent = this.parentNode; + + if ( jQuery.inArray( this, ignored ) < 0 ) { + jQuery.cleanData( getAll( this ) ); + if ( parent ) { + parent.replaceChild( elem, this ); + } + } + + // Force callback invocation + }, ignored ); + } +} ); + +jQuery.each( { + appendTo: "append", + prependTo: "prepend", + insertBefore: "before", + insertAfter: "after", + replaceAll: "replaceWith" +}, function( name, original ) { + jQuery.fn[ name ] = function( selector ) { + var elems, + ret = [], + insert = jQuery( selector ), + last = insert.length - 1, + i = 0; + + for ( ; i <= last; i++ ) { + elems = i === last ? this : this.clone( true ); + jQuery( insert[ i ] )[ original ]( elems ); + + // Support: Android <=4.0 only, PhantomJS 1 only + // .get() because push.apply(_, arraylike) throws on ancient WebKit + push.apply( ret, elems.get() ); + } + + return this.pushStack( ret ); + }; +} ); +var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" ); + +var getStyles = function( elem ) { + + // Support: IE <=11 only, Firefox <=30 (#15098, #14150) + // IE throws on elements created in popups + // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" + var view = elem.ownerDocument.defaultView; + + if ( !view || !view.opener ) { + view = window; + } + + return view.getComputedStyle( elem ); + }; + +var swap = function( elem, options, callback ) { + var ret, name, + old = {}; + + // Remember the old values, and insert the new ones + for ( name in options ) { + old[ name ] = elem.style[ name ]; + elem.style[ name ] = options[ name ]; + } + + ret = callback.call( elem ); + + // Revert the old values + for ( name in options ) { + elem.style[ name ] = old[ name ]; + } + + return ret; +}; + + +var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" ); + + + +( function() { + + // Executing both pixelPosition & boxSizingReliable tests require only one layout + // so they're executed at the same time to save the second computation. + function computeStyleTests() { + + // This is a singleton, we need to execute it only once + if ( !div ) { + return; + } + + container.style.cssText = "position:absolute;left:-11111px;width:60px;" + + "margin-top:1px;padding:0;border:0"; + div.style.cssText = + "position:relative;display:block;box-sizing:border-box;overflow:scroll;" + + "margin:auto;border:1px;padding:1px;" + + "width:60%;top:1%"; + documentElement.appendChild( container ).appendChild( div ); + + var divStyle = window.getComputedStyle( div ); + pixelPositionVal = divStyle.top !== "1%"; + + // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44 + reliableMarginLeftVal = roundPixelMeasures( divStyle.marginLeft ) === 12; + + // Support: Android 4.0 - 4.3 only, Safari <=9.1 - 10.1, iOS <=7.0 - 9.3 + // Some styles come back with percentage values, even though they shouldn't + div.style.right = "60%"; + pixelBoxStylesVal = roundPixelMeasures( divStyle.right ) === 36; + + // Support: IE 9 - 11 only + // Detect misreporting of content dimensions for box-sizing:border-box elements + boxSizingReliableVal = roundPixelMeasures( divStyle.width ) === 36; + + // Support: IE 9 only + // Detect overflow:scroll screwiness (gh-3699) + // Support: Chrome <=64 + // Don't get tricked when zoom affects offsetWidth (gh-4029) + div.style.position = "absolute"; + scrollboxSizeVal = roundPixelMeasures( div.offsetWidth / 3 ) === 12; + + documentElement.removeChild( container ); + + // Nullify the div so it wouldn't be stored in the memory and + // it will also be a sign that checks already performed + div = null; + } + + function roundPixelMeasures( measure ) { + return Math.round( parseFloat( measure ) ); + } + + var pixelPositionVal, boxSizingReliableVal, scrollboxSizeVal, pixelBoxStylesVal, + reliableTrDimensionsVal, reliableMarginLeftVal, + container = document.createElement( "div" ), + div = document.createElement( "div" ); + + // Finish early in limited (non-browser) environments + if ( !div.style ) { + return; + } + + // Support: IE <=9 - 11 only + // Style of cloned element affects source element cloned (#8908) + div.style.backgroundClip = "content-box"; + div.cloneNode( true ).style.backgroundClip = ""; + support.clearCloneStyle = div.style.backgroundClip === "content-box"; + + jQuery.extend( support, { + boxSizingReliable: function() { + computeStyleTests(); + return boxSizingReliableVal; + }, + pixelBoxStyles: function() { + computeStyleTests(); + return pixelBoxStylesVal; + }, + pixelPosition: function() { + computeStyleTests(); + return pixelPositionVal; + }, + reliableMarginLeft: function() { + computeStyleTests(); + return reliableMarginLeftVal; + }, + scrollboxSize: function() { + computeStyleTests(); + return scrollboxSizeVal; + }, + + // Support: IE 9 - 11+, Edge 15 - 18+ + // IE/Edge misreport `getComputedStyle` of table rows with width/height + // set in CSS while `offset*` properties report correct values. + // Behavior in IE 9 is more subtle than in newer versions & it passes + // some versions of this test; make sure not to make it pass there! + // + // Support: Firefox 70+ + // Only Firefox includes border widths + // in computed dimensions. (gh-4529) + reliableTrDimensions: function() { + var table, tr, trChild, trStyle; + if ( reliableTrDimensionsVal == null ) { + table = document.createElement( "table" ); + tr = document.createElement( "tr" ); + trChild = document.createElement( "div" ); + + table.style.cssText = "position:absolute;left:-11111px;border-collapse:separate"; + tr.style.cssText = "border:1px solid"; + + // Support: Chrome 86+ + // Height set through cssText does not get applied. + // Computed height then comes back as 0. + tr.style.height = "1px"; + trChild.style.height = "9px"; + + // Support: Android 8 Chrome 86+ + // In our bodyBackground.html iframe, + // display for all div elements is set to "inline", + // which causes a problem only in Android 8 Chrome 86. + // Ensuring the div is display: block + // gets around this issue. + trChild.style.display = "block"; + + documentElement + .appendChild( table ) + .appendChild( tr ) + .appendChild( trChild ); + + trStyle = window.getComputedStyle( tr ); + reliableTrDimensionsVal = ( parseInt( trStyle.height, 10 ) + + parseInt( trStyle.borderTopWidth, 10 ) + + parseInt( trStyle.borderBottomWidth, 10 ) ) === tr.offsetHeight; + + documentElement.removeChild( table ); + } + return reliableTrDimensionsVal; + } + } ); +} )(); + + +function curCSS( elem, name, computed ) { + var width, minWidth, maxWidth, ret, + + // Support: Firefox 51+ + // Retrieving style before computed somehow + // fixes an issue with getting wrong values + // on detached elements + style = elem.style; + + computed = computed || getStyles( elem ); + + // getPropertyValue is needed for: + // .css('filter') (IE 9 only, #12537) + // .css('--customProperty) (#3144) + if ( computed ) { + ret = computed.getPropertyValue( name ) || computed[ name ]; + + if ( ret === "" && !isAttached( elem ) ) { + ret = jQuery.style( elem, name ); + } + + // A tribute to the "awesome hack by Dean Edwards" + // Android Browser returns percentage for some values, + // but width seems to be reliably pixels. + // This is against the CSSOM draft spec: + // https://drafts.csswg.org/cssom/#resolved-values + if ( !support.pixelBoxStyles() && rnumnonpx.test( ret ) && rboxStyle.test( name ) ) { + + // Remember the original values + width = style.width; + minWidth = style.minWidth; + maxWidth = style.maxWidth; + + // Put in the new values to get a computed value out + style.minWidth = style.maxWidth = style.width = ret; + ret = computed.width; + + // Revert the changed values + style.width = width; + style.minWidth = minWidth; + style.maxWidth = maxWidth; + } + } + + return ret !== undefined ? + + // Support: IE <=9 - 11 only + // IE returns zIndex value as an integer. + ret + "" : + ret; +} + + +function addGetHookIf( conditionFn, hookFn ) { + + // Define the hook, we'll check on the first run if it's really needed. + return { + get: function() { + if ( conditionFn() ) { + + // Hook not needed (or it's not possible to use it due + // to missing dependency), remove it. + delete this.get; + return; + } + + // Hook needed; redefine it so that the support test is not executed again. + return ( this.get = hookFn ).apply( this, arguments ); + } + }; +} + + +var cssPrefixes = [ "Webkit", "Moz", "ms" ], + emptyStyle = document.createElement( "div" ).style, + vendorProps = {}; + +// Return a vendor-prefixed property or undefined +function vendorPropName( name ) { + + // Check for vendor prefixed names + var capName = name[ 0 ].toUpperCase() + name.slice( 1 ), + i = cssPrefixes.length; + + while ( i-- ) { + name = cssPrefixes[ i ] + capName; + if ( name in emptyStyle ) { + return name; + } + } +} + +// Return a potentially-mapped jQuery.cssProps or vendor prefixed property +function finalPropName( name ) { + var final = jQuery.cssProps[ name ] || vendorProps[ name ]; + + if ( final ) { + return final; + } + if ( name in emptyStyle ) { + return name; + } + return vendorProps[ name ] = vendorPropName( name ) || name; +} + + +var + + // Swappable if display is none or starts with table + // except "table", "table-cell", or "table-caption" + // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display + rdisplayswap = /^(none|table(?!-c[ea]).+)/, + rcustomProp = /^--/, + cssShow = { position: "absolute", visibility: "hidden", display: "block" }, + cssNormalTransform = { + letterSpacing: "0", + fontWeight: "400" + }; + +function setPositiveNumber( _elem, value, subtract ) { + + // Any relative (+/-) values have already been + // normalized at this point + var matches = rcssNum.exec( value ); + return matches ? + + // Guard against undefined "subtract", e.g., when used as in cssHooks + Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) : + value; +} + +function boxModelAdjustment( elem, dimension, box, isBorderBox, styles, computedVal ) { + var i = dimension === "width" ? 1 : 0, + extra = 0, + delta = 0; + + // Adjustment may not be necessary + if ( box === ( isBorderBox ? "border" : "content" ) ) { + return 0; + } + + for ( ; i < 4; i += 2 ) { + + // Both box models exclude margin + if ( box === "margin" ) { + delta += jQuery.css( elem, box + cssExpand[ i ], true, styles ); + } + + // If we get here with a content-box, we're seeking "padding" or "border" or "margin" + if ( !isBorderBox ) { + + // Add padding + delta += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + + // For "border" or "margin", add border + if ( box !== "padding" ) { + delta += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + + // But still keep track of it otherwise + } else { + extra += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + + // If we get here with a border-box (content + padding + border), we're seeking "content" or + // "padding" or "margin" + } else { + + // For "content", subtract padding + if ( box === "content" ) { + delta -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + } + + // For "content" or "padding", subtract border + if ( box !== "margin" ) { + delta -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + } + } + + // Account for positive content-box scroll gutter when requested by providing computedVal + if ( !isBorderBox && computedVal >= 0 ) { + + // offsetWidth/offsetHeight is a rounded sum of content, padding, scroll gutter, and border + // Assuming integer scroll gutter, subtract the rest and round down + delta += Math.max( 0, Math.ceil( + elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - + computedVal - + delta - + extra - + 0.5 + + // If offsetWidth/offsetHeight is unknown, then we can't determine content-box scroll gutter + // Use an explicit zero to avoid NaN (gh-3964) + ) ) || 0; + } + + return delta; +} + +function getWidthOrHeight( elem, dimension, extra ) { + + // Start with computed style + var styles = getStyles( elem ), + + // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-4322). + // Fake content-box until we know it's needed to know the true value. + boxSizingNeeded = !support.boxSizingReliable() || extra, + isBorderBox = boxSizingNeeded && + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + valueIsBorderBox = isBorderBox, + + val = curCSS( elem, dimension, styles ), + offsetProp = "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ); + + // Support: Firefox <=54 + // Return a confounding non-pixel value or feign ignorance, as appropriate. + if ( rnumnonpx.test( val ) ) { + if ( !extra ) { + return val; + } + val = "auto"; + } + + + // Support: IE 9 - 11 only + // Use offsetWidth/offsetHeight for when box sizing is unreliable. + // In those cases, the computed value can be trusted to be border-box. + if ( ( !support.boxSizingReliable() && isBorderBox || + + // Support: IE 10 - 11+, Edge 15 - 18+ + // IE/Edge misreport `getComputedStyle` of table rows with width/height + // set in CSS while `offset*` properties report correct values. + // Interestingly, in some cases IE 9 doesn't suffer from this issue. + !support.reliableTrDimensions() && nodeName( elem, "tr" ) || + + // Fall back to offsetWidth/offsetHeight when value is "auto" + // This happens for inline elements with no explicit setting (gh-3571) + val === "auto" || + + // Support: Android <=4.1 - 4.3 only + // Also use offsetWidth/offsetHeight for misreported inline dimensions (gh-3602) + !parseFloat( val ) && jQuery.css( elem, "display", false, styles ) === "inline" ) && + + // Make sure the element is visible & connected + elem.getClientRects().length ) { + + isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box"; + + // Where available, offsetWidth/offsetHeight approximate border box dimensions. + // Where not available (e.g., SVG), assume unreliable box-sizing and interpret the + // retrieved value as a content box dimension. + valueIsBorderBox = offsetProp in elem; + if ( valueIsBorderBox ) { + val = elem[ offsetProp ]; + } + } + + // Normalize "" and auto + val = parseFloat( val ) || 0; + + // Adjust for the element's box model + return ( val + + boxModelAdjustment( + elem, + dimension, + extra || ( isBorderBox ? "border" : "content" ), + valueIsBorderBox, + styles, + + // Provide the current computed size to request scroll gutter calculation (gh-3589) + val + ) + ) + "px"; +} + +jQuery.extend( { + + // Add in style property hooks for overriding the default + // behavior of getting and setting a style property + cssHooks: { + opacity: { + get: function( elem, computed ) { + if ( computed ) { + + // We should always get a number back from opacity + var ret = curCSS( elem, "opacity" ); + return ret === "" ? "1" : ret; + } + } + } + }, + + // Don't automatically add "px" to these possibly-unitless properties + cssNumber: { + "animationIterationCount": true, + "columnCount": true, + "fillOpacity": true, + "flexGrow": true, + "flexShrink": true, + "fontWeight": true, + "gridArea": true, + "gridColumn": true, + "gridColumnEnd": true, + "gridColumnStart": true, + "gridRow": true, + "gridRowEnd": true, + "gridRowStart": true, + "lineHeight": true, + "opacity": true, + "order": true, + "orphans": true, + "widows": true, + "zIndex": true, + "zoom": true + }, + + // Add in properties whose names you wish to fix before + // setting or getting the value + cssProps: {}, + + // Get and set the style property on a DOM Node + style: function( elem, name, value, extra ) { + + // Don't set styles on text and comment nodes + if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) { + return; + } + + // Make sure that we're working with the right name + var ret, type, hooks, + origName = camelCase( name ), + isCustomProp = rcustomProp.test( name ), + style = elem.style; + + // Make sure that we're working with the right name. We don't + // want to query the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Gets hook for the prefixed version, then unprefixed version + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // Check if we're setting a value + if ( value !== undefined ) { + type = typeof value; + + // Convert "+=" or "-=" to relative numbers (#7345) + if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) { + value = adjustCSS( elem, name, ret ); + + // Fixes bug #9237 + type = "number"; + } + + // Make sure that null and NaN values aren't set (#7116) + if ( value == null || value !== value ) { + return; + } + + // If a number was passed in, add the unit (except for certain CSS properties) + // The isCustomProp check can be removed in jQuery 4.0 when we only auto-append + // "px" to a few hardcoded values. + if ( type === "number" && !isCustomProp ) { + value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" ); + } + + // background-* props affect original clone's values + if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) { + style[ name ] = "inherit"; + } + + // If a hook was provided, use that value, otherwise just set the specified value + if ( !hooks || !( "set" in hooks ) || + ( value = hooks.set( elem, value, extra ) ) !== undefined ) { + + if ( isCustomProp ) { + style.setProperty( name, value ); + } else { + style[ name ] = value; + } + } + + } else { + + // If a hook was provided get the non-computed value from there + if ( hooks && "get" in hooks && + ( ret = hooks.get( elem, false, extra ) ) !== undefined ) { + + return ret; + } + + // Otherwise just get the value from the style object + return style[ name ]; + } + }, + + css: function( elem, name, extra, styles ) { + var val, num, hooks, + origName = camelCase( name ), + isCustomProp = rcustomProp.test( name ); + + // Make sure that we're working with the right name. We don't + // want to modify the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Try prefixed name followed by the unprefixed name + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // If a hook was provided get the computed value from there + if ( hooks && "get" in hooks ) { + val = hooks.get( elem, true, extra ); + } + + // Otherwise, if a way to get the computed value exists, use that + if ( val === undefined ) { + val = curCSS( elem, name, styles ); + } + + // Convert "normal" to computed value + if ( val === "normal" && name in cssNormalTransform ) { + val = cssNormalTransform[ name ]; + } + + // Make numeric if forced or a qualifier was provided and val looks numeric + if ( extra === "" || extra ) { + num = parseFloat( val ); + return extra === true || isFinite( num ) ? num || 0 : val; + } + + return val; + } +} ); + +jQuery.each( [ "height", "width" ], function( _i, dimension ) { + jQuery.cssHooks[ dimension ] = { + get: function( elem, computed, extra ) { + if ( computed ) { + + // Certain elements can have dimension info if we invisibly show them + // but it must have a current display style that would benefit + return rdisplayswap.test( jQuery.css( elem, "display" ) ) && + + // Support: Safari 8+ + // Table columns in Safari have non-zero offsetWidth & zero + // getBoundingClientRect().width unless display is changed. + // Support: IE <=11 only + // Running getBoundingClientRect on a disconnected node + // in IE throws an error. + ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ? + swap( elem, cssShow, function() { + return getWidthOrHeight( elem, dimension, extra ); + } ) : + getWidthOrHeight( elem, dimension, extra ); + } + }, + + set: function( elem, value, extra ) { + var matches, + styles = getStyles( elem ), + + // Only read styles.position if the test has a chance to fail + // to avoid forcing a reflow. + scrollboxSizeBuggy = !support.scrollboxSize() && + styles.position === "absolute", + + // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-3991) + boxSizingNeeded = scrollboxSizeBuggy || extra, + isBorderBox = boxSizingNeeded && + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + subtract = extra ? + boxModelAdjustment( + elem, + dimension, + extra, + isBorderBox, + styles + ) : + 0; + + // Account for unreliable border-box dimensions by comparing offset* to computed and + // faking a content-box to get border and padding (gh-3699) + if ( isBorderBox && scrollboxSizeBuggy ) { + subtract -= Math.ceil( + elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - + parseFloat( styles[ dimension ] ) - + boxModelAdjustment( elem, dimension, "border", false, styles ) - + 0.5 + ); + } + + // Convert to pixels if value adjustment is needed + if ( subtract && ( matches = rcssNum.exec( value ) ) && + ( matches[ 3 ] || "px" ) !== "px" ) { + + elem.style[ dimension ] = value; + value = jQuery.css( elem, dimension ); + } + + return setPositiveNumber( elem, value, subtract ); + } + }; +} ); + +jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft, + function( elem, computed ) { + if ( computed ) { + return ( parseFloat( curCSS( elem, "marginLeft" ) ) || + elem.getBoundingClientRect().left - + swap( elem, { marginLeft: 0 }, function() { + return elem.getBoundingClientRect().left; + } ) + ) + "px"; + } + } +); + +// These hooks are used by animate to expand properties +jQuery.each( { + margin: "", + padding: "", + border: "Width" +}, function( prefix, suffix ) { + jQuery.cssHooks[ prefix + suffix ] = { + expand: function( value ) { + var i = 0, + expanded = {}, + + // Assumes a single number if not a string + parts = typeof value === "string" ? value.split( " " ) : [ value ]; + + for ( ; i < 4; i++ ) { + expanded[ prefix + cssExpand[ i ] + suffix ] = + parts[ i ] || parts[ i - 2 ] || parts[ 0 ]; + } + + return expanded; + } + }; + + if ( prefix !== "margin" ) { + jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber; + } +} ); + +jQuery.fn.extend( { + css: function( name, value ) { + return access( this, function( elem, name, value ) { + var styles, len, + map = {}, + i = 0; + + if ( Array.isArray( name ) ) { + styles = getStyles( elem ); + len = name.length; + + for ( ; i < len; i++ ) { + map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles ); + } + + return map; + } + + return value !== undefined ? + jQuery.style( elem, name, value ) : + jQuery.css( elem, name ); + }, name, value, arguments.length > 1 ); + } +} ); + + +function Tween( elem, options, prop, end, easing ) { + return new Tween.prototype.init( elem, options, prop, end, easing ); +} +jQuery.Tween = Tween; + +Tween.prototype = { + constructor: Tween, + init: function( elem, options, prop, end, easing, unit ) { + this.elem = elem; + this.prop = prop; + this.easing = easing || jQuery.easing._default; + this.options = options; + this.start = this.now = this.cur(); + this.end = end; + this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" ); + }, + cur: function() { + var hooks = Tween.propHooks[ this.prop ]; + + return hooks && hooks.get ? + hooks.get( this ) : + Tween.propHooks._default.get( this ); + }, + run: function( percent ) { + var eased, + hooks = Tween.propHooks[ this.prop ]; + + if ( this.options.duration ) { + this.pos = eased = jQuery.easing[ this.easing ]( + percent, this.options.duration * percent, 0, 1, this.options.duration + ); + } else { + this.pos = eased = percent; + } + this.now = ( this.end - this.start ) * eased + this.start; + + if ( this.options.step ) { + this.options.step.call( this.elem, this.now, this ); + } + + if ( hooks && hooks.set ) { + hooks.set( this ); + } else { + Tween.propHooks._default.set( this ); + } + return this; + } +}; + +Tween.prototype.init.prototype = Tween.prototype; + +Tween.propHooks = { + _default: { + get: function( tween ) { + var result; + + // Use a property on the element directly when it is not a DOM element, + // or when there is no matching style property that exists. + if ( tween.elem.nodeType !== 1 || + tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) { + return tween.elem[ tween.prop ]; + } + + // Passing an empty string as a 3rd parameter to .css will automatically + // attempt a parseFloat and fallback to a string if the parse fails. + // Simple values such as "10px" are parsed to Float; + // complex values such as "rotate(1rad)" are returned as-is. + result = jQuery.css( tween.elem, tween.prop, "" ); + + // Empty strings, null, undefined and "auto" are converted to 0. + return !result || result === "auto" ? 0 : result; + }, + set: function( tween ) { + + // Use step hook for back compat. + // Use cssHook if its there. + // Use .style if available and use plain properties where available. + if ( jQuery.fx.step[ tween.prop ] ) { + jQuery.fx.step[ tween.prop ]( tween ); + } else if ( tween.elem.nodeType === 1 && ( + jQuery.cssHooks[ tween.prop ] || + tween.elem.style[ finalPropName( tween.prop ) ] != null ) ) { + jQuery.style( tween.elem, tween.prop, tween.now + tween.unit ); + } else { + tween.elem[ tween.prop ] = tween.now; + } + } + } +}; + +// Support: IE <=9 only +// Panic based approach to setting things on disconnected nodes +Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = { + set: function( tween ) { + if ( tween.elem.nodeType && tween.elem.parentNode ) { + tween.elem[ tween.prop ] = tween.now; + } + } +}; + +jQuery.easing = { + linear: function( p ) { + return p; + }, + swing: function( p ) { + return 0.5 - Math.cos( p * Math.PI ) / 2; + }, + _default: "swing" +}; + +jQuery.fx = Tween.prototype.init; + +// Back compat <1.8 extension point +jQuery.fx.step = {}; + + + + +var + fxNow, inProgress, + rfxtypes = /^(?:toggle|show|hide)$/, + rrun = /queueHooks$/; + +function schedule() { + if ( inProgress ) { + if ( document.hidden === false && window.requestAnimationFrame ) { + window.requestAnimationFrame( schedule ); + } else { + window.setTimeout( schedule, jQuery.fx.interval ); + } + + jQuery.fx.tick(); + } +} + +// Animations created synchronously will run synchronously +function createFxNow() { + window.setTimeout( function() { + fxNow = undefined; + } ); + return ( fxNow = Date.now() ); +} + +// Generate parameters to create a standard animation +function genFx( type, includeWidth ) { + var which, + i = 0, + attrs = { height: type }; + + // If we include width, step value is 1 to do all cssExpand values, + // otherwise step value is 2 to skip over Left and Right + includeWidth = includeWidth ? 1 : 0; + for ( ; i < 4; i += 2 - includeWidth ) { + which = cssExpand[ i ]; + attrs[ "margin" + which ] = attrs[ "padding" + which ] = type; + } + + if ( includeWidth ) { + attrs.opacity = attrs.width = type; + } + + return attrs; +} + +function createTween( value, prop, animation ) { + var tween, + collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ), + index = 0, + length = collection.length; + for ( ; index < length; index++ ) { + if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) { + + // We're done with this property + return tween; + } + } +} + +function defaultPrefilter( elem, props, opts ) { + var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display, + isBox = "width" in props || "height" in props, + anim = this, + orig = {}, + style = elem.style, + hidden = elem.nodeType && isHiddenWithinTree( elem ), + dataShow = dataPriv.get( elem, "fxshow" ); + + // Queue-skipping animations hijack the fx hooks + if ( !opts.queue ) { + hooks = jQuery._queueHooks( elem, "fx" ); + if ( hooks.unqueued == null ) { + hooks.unqueued = 0; + oldfire = hooks.empty.fire; + hooks.empty.fire = function() { + if ( !hooks.unqueued ) { + oldfire(); + } + }; + } + hooks.unqueued++; + + anim.always( function() { + + // Ensure the complete handler is called before this completes + anim.always( function() { + hooks.unqueued--; + if ( !jQuery.queue( elem, "fx" ).length ) { + hooks.empty.fire(); + } + } ); + } ); + } + + // Detect show/hide animations + for ( prop in props ) { + value = props[ prop ]; + if ( rfxtypes.test( value ) ) { + delete props[ prop ]; + toggle = toggle || value === "toggle"; + if ( value === ( hidden ? "hide" : "show" ) ) { + + // Pretend to be hidden if this is a "show" and + // there is still data from a stopped show/hide + if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) { + hidden = true; + + // Ignore all other no-op show/hide data + } else { + continue; + } + } + orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop ); + } + } + + // Bail out if this is a no-op like .hide().hide() + propTween = !jQuery.isEmptyObject( props ); + if ( !propTween && jQuery.isEmptyObject( orig ) ) { + return; + } + + // Restrict "overflow" and "display" styles during box animations + if ( isBox && elem.nodeType === 1 ) { + + // Support: IE <=9 - 11, Edge 12 - 15 + // Record all 3 overflow attributes because IE does not infer the shorthand + // from identically-valued overflowX and overflowY and Edge just mirrors + // the overflowX value there. + opts.overflow = [ style.overflow, style.overflowX, style.overflowY ]; + + // Identify a display type, preferring old show/hide data over the CSS cascade + restoreDisplay = dataShow && dataShow.display; + if ( restoreDisplay == null ) { + restoreDisplay = dataPriv.get( elem, "display" ); + } + display = jQuery.css( elem, "display" ); + if ( display === "none" ) { + if ( restoreDisplay ) { + display = restoreDisplay; + } else { + + // Get nonempty value(s) by temporarily forcing visibility + showHide( [ elem ], true ); + restoreDisplay = elem.style.display || restoreDisplay; + display = jQuery.css( elem, "display" ); + showHide( [ elem ] ); + } + } + + // Animate inline elements as inline-block + if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) { + if ( jQuery.css( elem, "float" ) === "none" ) { + + // Restore the original display value at the end of pure show/hide animations + if ( !propTween ) { + anim.done( function() { + style.display = restoreDisplay; + } ); + if ( restoreDisplay == null ) { + display = style.display; + restoreDisplay = display === "none" ? "" : display; + } + } + style.display = "inline-block"; + } + } + } + + if ( opts.overflow ) { + style.overflow = "hidden"; + anim.always( function() { + style.overflow = opts.overflow[ 0 ]; + style.overflowX = opts.overflow[ 1 ]; + style.overflowY = opts.overflow[ 2 ]; + } ); + } + + // Implement show/hide animations + propTween = false; + for ( prop in orig ) { + + // General show/hide setup for this element animation + if ( !propTween ) { + if ( dataShow ) { + if ( "hidden" in dataShow ) { + hidden = dataShow.hidden; + } + } else { + dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } ); + } + + // Store hidden/visible for toggle so `.stop().toggle()` "reverses" + if ( toggle ) { + dataShow.hidden = !hidden; + } + + // Show elements before animating them + if ( hidden ) { + showHide( [ elem ], true ); + } + + /* eslint-disable no-loop-func */ + + anim.done( function() { + + /* eslint-enable no-loop-func */ + + // The final step of a "hide" animation is actually hiding the element + if ( !hidden ) { + showHide( [ elem ] ); + } + dataPriv.remove( elem, "fxshow" ); + for ( prop in orig ) { + jQuery.style( elem, prop, orig[ prop ] ); + } + } ); + } + + // Per-property setup + propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim ); + if ( !( prop in dataShow ) ) { + dataShow[ prop ] = propTween.start; + if ( hidden ) { + propTween.end = propTween.start; + propTween.start = 0; + } + } + } +} + +function propFilter( props, specialEasing ) { + var index, name, easing, value, hooks; + + // camelCase, specialEasing and expand cssHook pass + for ( index in props ) { + name = camelCase( index ); + easing = specialEasing[ name ]; + value = props[ index ]; + if ( Array.isArray( value ) ) { + easing = value[ 1 ]; + value = props[ index ] = value[ 0 ]; + } + + if ( index !== name ) { + props[ name ] = value; + delete props[ index ]; + } + + hooks = jQuery.cssHooks[ name ]; + if ( hooks && "expand" in hooks ) { + value = hooks.expand( value ); + delete props[ name ]; + + // Not quite $.extend, this won't overwrite existing keys. + // Reusing 'index' because we have the correct "name" + for ( index in value ) { + if ( !( index in props ) ) { + props[ index ] = value[ index ]; + specialEasing[ index ] = easing; + } + } + } else { + specialEasing[ name ] = easing; + } + } +} + +function Animation( elem, properties, options ) { + var result, + stopped, + index = 0, + length = Animation.prefilters.length, + deferred = jQuery.Deferred().always( function() { + + // Don't match elem in the :animated selector + delete tick.elem; + } ), + tick = function() { + if ( stopped ) { + return false; + } + var currentTime = fxNow || createFxNow(), + remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ), + + // Support: Android 2.3 only + // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497) + temp = remaining / animation.duration || 0, + percent = 1 - temp, + index = 0, + length = animation.tweens.length; + + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( percent ); + } + + deferred.notifyWith( elem, [ animation, percent, remaining ] ); + + // If there's more to do, yield + if ( percent < 1 && length ) { + return remaining; + } + + // If this was an empty animation, synthesize a final progress notification + if ( !length ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + } + + // Resolve the animation and report its conclusion + deferred.resolveWith( elem, [ animation ] ); + return false; + }, + animation = deferred.promise( { + elem: elem, + props: jQuery.extend( {}, properties ), + opts: jQuery.extend( true, { + specialEasing: {}, + easing: jQuery.easing._default + }, options ), + originalProperties: properties, + originalOptions: options, + startTime: fxNow || createFxNow(), + duration: options.duration, + tweens: [], + createTween: function( prop, end ) { + var tween = jQuery.Tween( elem, animation.opts, prop, end, + animation.opts.specialEasing[ prop ] || animation.opts.easing ); + animation.tweens.push( tween ); + return tween; + }, + stop: function( gotoEnd ) { + var index = 0, + + // If we are going to the end, we want to run all the tweens + // otherwise we skip this part + length = gotoEnd ? animation.tweens.length : 0; + if ( stopped ) { + return this; + } + stopped = true; + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( 1 ); + } + + // Resolve when we played the last frame; otherwise, reject + if ( gotoEnd ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + deferred.resolveWith( elem, [ animation, gotoEnd ] ); + } else { + deferred.rejectWith( elem, [ animation, gotoEnd ] ); + } + return this; + } + } ), + props = animation.props; + + propFilter( props, animation.opts.specialEasing ); + + for ( ; index < length; index++ ) { + result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts ); + if ( result ) { + if ( isFunction( result.stop ) ) { + jQuery._queueHooks( animation.elem, animation.opts.queue ).stop = + result.stop.bind( result ); + } + return result; + } + } + + jQuery.map( props, createTween, animation ); + + if ( isFunction( animation.opts.start ) ) { + animation.opts.start.call( elem, animation ); + } + + // Attach callbacks from options + animation + .progress( animation.opts.progress ) + .done( animation.opts.done, animation.opts.complete ) + .fail( animation.opts.fail ) + .always( animation.opts.always ); + + jQuery.fx.timer( + jQuery.extend( tick, { + elem: elem, + anim: animation, + queue: animation.opts.queue + } ) + ); + + return animation; +} + +jQuery.Animation = jQuery.extend( Animation, { + + tweeners: { + "*": [ function( prop, value ) { + var tween = this.createTween( prop, value ); + adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween ); + return tween; + } ] + }, + + tweener: function( props, callback ) { + if ( isFunction( props ) ) { + callback = props; + props = [ "*" ]; + } else { + props = props.match( rnothtmlwhite ); + } + + var prop, + index = 0, + length = props.length; + + for ( ; index < length; index++ ) { + prop = props[ index ]; + Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || []; + Animation.tweeners[ prop ].unshift( callback ); + } + }, + + prefilters: [ defaultPrefilter ], + + prefilter: function( callback, prepend ) { + if ( prepend ) { + Animation.prefilters.unshift( callback ); + } else { + Animation.prefilters.push( callback ); + } + } +} ); + +jQuery.speed = function( speed, easing, fn ) { + var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : { + complete: fn || !fn && easing || + isFunction( speed ) && speed, + duration: speed, + easing: fn && easing || easing && !isFunction( easing ) && easing + }; + + // Go to the end state if fx are off + if ( jQuery.fx.off ) { + opt.duration = 0; + + } else { + if ( typeof opt.duration !== "number" ) { + if ( opt.duration in jQuery.fx.speeds ) { + opt.duration = jQuery.fx.speeds[ opt.duration ]; + + } else { + opt.duration = jQuery.fx.speeds._default; + } + } + } + + // Normalize opt.queue - true/undefined/null -> "fx" + if ( opt.queue == null || opt.queue === true ) { + opt.queue = "fx"; + } + + // Queueing + opt.old = opt.complete; + + opt.complete = function() { + if ( isFunction( opt.old ) ) { + opt.old.call( this ); + } + + if ( opt.queue ) { + jQuery.dequeue( this, opt.queue ); + } + }; + + return opt; +}; + +jQuery.fn.extend( { + fadeTo: function( speed, to, easing, callback ) { + + // Show any hidden elements after setting opacity to 0 + return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show() + + // Animate to the value specified + .end().animate( { opacity: to }, speed, easing, callback ); + }, + animate: function( prop, speed, easing, callback ) { + var empty = jQuery.isEmptyObject( prop ), + optall = jQuery.speed( speed, easing, callback ), + doAnimation = function() { + + // Operate on a copy of prop so per-property easing won't be lost + var anim = Animation( this, jQuery.extend( {}, prop ), optall ); + + // Empty animations, or finishing resolves immediately + if ( empty || dataPriv.get( this, "finish" ) ) { + anim.stop( true ); + } + }; + + doAnimation.finish = doAnimation; + + return empty || optall.queue === false ? + this.each( doAnimation ) : + this.queue( optall.queue, doAnimation ); + }, + stop: function( type, clearQueue, gotoEnd ) { + var stopQueue = function( hooks ) { + var stop = hooks.stop; + delete hooks.stop; + stop( gotoEnd ); + }; + + if ( typeof type !== "string" ) { + gotoEnd = clearQueue; + clearQueue = type; + type = undefined; + } + if ( clearQueue ) { + this.queue( type || "fx", [] ); + } + + return this.each( function() { + var dequeue = true, + index = type != null && type + "queueHooks", + timers = jQuery.timers, + data = dataPriv.get( this ); + + if ( index ) { + if ( data[ index ] && data[ index ].stop ) { + stopQueue( data[ index ] ); + } + } else { + for ( index in data ) { + if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) { + stopQueue( data[ index ] ); + } + } + } + + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && + ( type == null || timers[ index ].queue === type ) ) { + + timers[ index ].anim.stop( gotoEnd ); + dequeue = false; + timers.splice( index, 1 ); + } + } + + // Start the next in the queue if the last step wasn't forced. + // Timers currently will call their complete callbacks, which + // will dequeue but only if they were gotoEnd. + if ( dequeue || !gotoEnd ) { + jQuery.dequeue( this, type ); + } + } ); + }, + finish: function( type ) { + if ( type !== false ) { + type = type || "fx"; + } + return this.each( function() { + var index, + data = dataPriv.get( this ), + queue = data[ type + "queue" ], + hooks = data[ type + "queueHooks" ], + timers = jQuery.timers, + length = queue ? queue.length : 0; + + // Enable finishing flag on private data + data.finish = true; + + // Empty the queue first + jQuery.queue( this, type, [] ); + + if ( hooks && hooks.stop ) { + hooks.stop.call( this, true ); + } + + // Look for any active animations, and finish them + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && timers[ index ].queue === type ) { + timers[ index ].anim.stop( true ); + timers.splice( index, 1 ); + } + } + + // Look for any animations in the old queue and finish them + for ( index = 0; index < length; index++ ) { + if ( queue[ index ] && queue[ index ].finish ) { + queue[ index ].finish.call( this ); + } + } + + // Turn off finishing flag + delete data.finish; + } ); + } +} ); + +jQuery.each( [ "toggle", "show", "hide" ], function( _i, name ) { + var cssFn = jQuery.fn[ name ]; + jQuery.fn[ name ] = function( speed, easing, callback ) { + return speed == null || typeof speed === "boolean" ? + cssFn.apply( this, arguments ) : + this.animate( genFx( name, true ), speed, easing, callback ); + }; +} ); + +// Generate shortcuts for custom animations +jQuery.each( { + slideDown: genFx( "show" ), + slideUp: genFx( "hide" ), + slideToggle: genFx( "toggle" ), + fadeIn: { opacity: "show" }, + fadeOut: { opacity: "hide" }, + fadeToggle: { opacity: "toggle" } +}, function( name, props ) { + jQuery.fn[ name ] = function( speed, easing, callback ) { + return this.animate( props, speed, easing, callback ); + }; +} ); + +jQuery.timers = []; +jQuery.fx.tick = function() { + var timer, + i = 0, + timers = jQuery.timers; + + fxNow = Date.now(); + + for ( ; i < timers.length; i++ ) { + timer = timers[ i ]; + + // Run the timer and safely remove it when done (allowing for external removal) + if ( !timer() && timers[ i ] === timer ) { + timers.splice( i--, 1 ); + } + } + + if ( !timers.length ) { + jQuery.fx.stop(); + } + fxNow = undefined; +}; + +jQuery.fx.timer = function( timer ) { + jQuery.timers.push( timer ); + jQuery.fx.start(); +}; + +jQuery.fx.interval = 13; +jQuery.fx.start = function() { + if ( inProgress ) { + return; + } + + inProgress = true; + schedule(); +}; + +jQuery.fx.stop = function() { + inProgress = null; +}; + +jQuery.fx.speeds = { + slow: 600, + fast: 200, + + // Default speed + _default: 400 +}; + + +// Based off of the plugin by Clint Helfers, with permission. +// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/ +jQuery.fn.delay = function( time, type ) { + time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; + type = type || "fx"; + + return this.queue( type, function( next, hooks ) { + var timeout = window.setTimeout( next, time ); + hooks.stop = function() { + window.clearTimeout( timeout ); + }; + } ); +}; + + +( function() { + var input = document.createElement( "input" ), + select = document.createElement( "select" ), + opt = select.appendChild( document.createElement( "option" ) ); + + input.type = "checkbox"; + + // Support: Android <=4.3 only + // Default value for a checkbox should be "on" + support.checkOn = input.value !== ""; + + // Support: IE <=11 only + // Must access selectedIndex to make default options select + support.optSelected = opt.selected; + + // Support: IE <=11 only + // An input loses its value after becoming a radio + input = document.createElement( "input" ); + input.value = "t"; + input.type = "radio"; + support.radioValue = input.value === "t"; +} )(); + + +var boolHook, + attrHandle = jQuery.expr.attrHandle; + +jQuery.fn.extend( { + attr: function( name, value ) { + return access( this, jQuery.attr, name, value, arguments.length > 1 ); + }, + + removeAttr: function( name ) { + return this.each( function() { + jQuery.removeAttr( this, name ); + } ); + } +} ); + +jQuery.extend( { + attr: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set attributes on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + // Fallback to prop when attributes are not supported + if ( typeof elem.getAttribute === "undefined" ) { + return jQuery.prop( elem, name, value ); + } + + // Attribute hooks are determined by the lowercase version + // Grab necessary hook if one is defined + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + hooks = jQuery.attrHooks[ name.toLowerCase() ] || + ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined ); + } + + if ( value !== undefined ) { + if ( value === null ) { + jQuery.removeAttr( elem, name ); + return; + } + + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + elem.setAttribute( name, value + "" ); + return value; + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + ret = jQuery.find.attr( elem, name ); + + // Non-existent attributes return null, we normalize to undefined + return ret == null ? undefined : ret; + }, + + attrHooks: { + type: { + set: function( elem, value ) { + if ( !support.radioValue && value === "radio" && + nodeName( elem, "input" ) ) { + var val = elem.value; + elem.setAttribute( "type", value ); + if ( val ) { + elem.value = val; + } + return value; + } + } + } + }, + + removeAttr: function( elem, value ) { + var name, + i = 0, + + // Attribute names can contain non-HTML whitespace characters + // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2 + attrNames = value && value.match( rnothtmlwhite ); + + if ( attrNames && elem.nodeType === 1 ) { + while ( ( name = attrNames[ i++ ] ) ) { + elem.removeAttribute( name ); + } + } + } +} ); + +// Hooks for boolean attributes +boolHook = { + set: function( elem, value, name ) { + if ( value === false ) { + + // Remove boolean attributes when set to false + jQuery.removeAttr( elem, name ); + } else { + elem.setAttribute( name, name ); + } + return name; + } +}; + +jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( _i, name ) { + var getter = attrHandle[ name ] || jQuery.find.attr; + + attrHandle[ name ] = function( elem, name, isXML ) { + var ret, handle, + lowercaseName = name.toLowerCase(); + + if ( !isXML ) { + + // Avoid an infinite loop by temporarily removing this function from the getter + handle = attrHandle[ lowercaseName ]; + attrHandle[ lowercaseName ] = ret; + ret = getter( elem, name, isXML ) != null ? + lowercaseName : + null; + attrHandle[ lowercaseName ] = handle; + } + return ret; + }; +} ); + + + + +var rfocusable = /^(?:input|select|textarea|button)$/i, + rclickable = /^(?:a|area)$/i; + +jQuery.fn.extend( { + prop: function( name, value ) { + return access( this, jQuery.prop, name, value, arguments.length > 1 ); + }, + + removeProp: function( name ) { + return this.each( function() { + delete this[ jQuery.propFix[ name ] || name ]; + } ); + } +} ); + +jQuery.extend( { + prop: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set properties on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + + // Fix name and attach hooks + name = jQuery.propFix[ name ] || name; + hooks = jQuery.propHooks[ name ]; + } + + if ( value !== undefined ) { + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + return ( elem[ name ] = value ); + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + return elem[ name ]; + }, + + propHooks: { + tabIndex: { + get: function( elem ) { + + // Support: IE <=9 - 11 only + // elem.tabIndex doesn't always return the + // correct value when it hasn't been explicitly set + // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ + // Use proper attribute retrieval(#12072) + var tabindex = jQuery.find.attr( elem, "tabindex" ); + + if ( tabindex ) { + return parseInt( tabindex, 10 ); + } + + if ( + rfocusable.test( elem.nodeName ) || + rclickable.test( elem.nodeName ) && + elem.href + ) { + return 0; + } + + return -1; + } + } + }, + + propFix: { + "for": "htmlFor", + "class": "className" + } +} ); + +// Support: IE <=11 only +// Accessing the selectedIndex property +// forces the browser to respect setting selected +// on the option +// The getter ensures a default option is selected +// when in an optgroup +// eslint rule "no-unused-expressions" is disabled for this code +// since it considers such accessions noop +if ( !support.optSelected ) { + jQuery.propHooks.selected = { + get: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent && parent.parentNode ) { + parent.parentNode.selectedIndex; + } + return null; + }, + set: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent ) { + parent.selectedIndex; + + if ( parent.parentNode ) { + parent.parentNode.selectedIndex; + } + } + } + }; +} + +jQuery.each( [ + "tabIndex", + "readOnly", + "maxLength", + "cellSpacing", + "cellPadding", + "rowSpan", + "colSpan", + "useMap", + "frameBorder", + "contentEditable" +], function() { + jQuery.propFix[ this.toLowerCase() ] = this; +} ); + + + + + // Strip and collapse whitespace according to HTML spec + // https://infra.spec.whatwg.org/#strip-and-collapse-ascii-whitespace + function stripAndCollapse( value ) { + var tokens = value.match( rnothtmlwhite ) || []; + return tokens.join( " " ); + } + + +function getClass( elem ) { + return elem.getAttribute && elem.getAttribute( "class" ) || ""; +} + +function classesToArray( value ) { + if ( Array.isArray( value ) ) { + return value; + } + if ( typeof value === "string" ) { + return value.match( rnothtmlwhite ) || []; + } + return []; +} + +jQuery.fn.extend( { + addClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).addClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + classes = classesToArray( value ); + + if ( classes.length ) { + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + if ( cur.indexOf( " " + clazz + " " ) < 0 ) { + cur += clazz + " "; + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + removeClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + if ( !arguments.length ) { + return this.attr( "class", "" ); + } + + classes = classesToArray( value ); + + if ( classes.length ) { + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + + // This expression is here for better compressibility (see addClass) + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + + // Remove *all* instances + while ( cur.indexOf( " " + clazz + " " ) > -1 ) { + cur = cur.replace( " " + clazz + " ", " " ); + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + toggleClass: function( value, stateVal ) { + var type = typeof value, + isValidValue = type === "string" || Array.isArray( value ); + + if ( typeof stateVal === "boolean" && isValidValue ) { + return stateVal ? this.addClass( value ) : this.removeClass( value ); + } + + if ( isFunction( value ) ) { + return this.each( function( i ) { + jQuery( this ).toggleClass( + value.call( this, i, getClass( this ), stateVal ), + stateVal + ); + } ); + } + + return this.each( function() { + var className, i, self, classNames; + + if ( isValidValue ) { + + // Toggle individual class names + i = 0; + self = jQuery( this ); + classNames = classesToArray( value ); + + while ( ( className = classNames[ i++ ] ) ) { + + // Check each className given, space separated list + if ( self.hasClass( className ) ) { + self.removeClass( className ); + } else { + self.addClass( className ); + } + } + + // Toggle whole class name + } else if ( value === undefined || type === "boolean" ) { + className = getClass( this ); + if ( className ) { + + // Store className if set + dataPriv.set( this, "__className__", className ); + } + + // If the element has a class name or if we're passed `false`, + // then remove the whole classname (if there was one, the above saved it). + // Otherwise bring back whatever was previously saved (if anything), + // falling back to the empty string if nothing was stored. + if ( this.setAttribute ) { + this.setAttribute( "class", + className || value === false ? + "" : + dataPriv.get( this, "__className__" ) || "" + ); + } + } + } ); + }, + + hasClass: function( selector ) { + var className, elem, + i = 0; + + className = " " + selector + " "; + while ( ( elem = this[ i++ ] ) ) { + if ( elem.nodeType === 1 && + ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) { + return true; + } + } + + return false; + } +} ); + + + + +var rreturn = /\r/g; + +jQuery.fn.extend( { + val: function( value ) { + var hooks, ret, valueIsFunction, + elem = this[ 0 ]; + + if ( !arguments.length ) { + if ( elem ) { + hooks = jQuery.valHooks[ elem.type ] || + jQuery.valHooks[ elem.nodeName.toLowerCase() ]; + + if ( hooks && + "get" in hooks && + ( ret = hooks.get( elem, "value" ) ) !== undefined + ) { + return ret; + } + + ret = elem.value; + + // Handle most common string cases + if ( typeof ret === "string" ) { + return ret.replace( rreturn, "" ); + } + + // Handle cases where value is null/undef or number + return ret == null ? "" : ret; + } + + return; + } + + valueIsFunction = isFunction( value ); + + return this.each( function( i ) { + var val; + + if ( this.nodeType !== 1 ) { + return; + } + + if ( valueIsFunction ) { + val = value.call( this, i, jQuery( this ).val() ); + } else { + val = value; + } + + // Treat null/undefined as ""; convert numbers to string + if ( val == null ) { + val = ""; + + } else if ( typeof val === "number" ) { + val += ""; + + } else if ( Array.isArray( val ) ) { + val = jQuery.map( val, function( value ) { + return value == null ? "" : value + ""; + } ); + } + + hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; + + // If set returns undefined, fall back to normal setting + if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) { + this.value = val; + } + } ); + } +} ); + +jQuery.extend( { + valHooks: { + option: { + get: function( elem ) { + + var val = jQuery.find.attr( elem, "value" ); + return val != null ? + val : + + // Support: IE <=10 - 11 only + // option.text throws exceptions (#14686, #14858) + // Strip and collapse whitespace + // https://html.spec.whatwg.org/#strip-and-collapse-whitespace + stripAndCollapse( jQuery.text( elem ) ); + } + }, + select: { + get: function( elem ) { + var value, option, i, + options = elem.options, + index = elem.selectedIndex, + one = elem.type === "select-one", + values = one ? null : [], + max = one ? index + 1 : options.length; + + if ( index < 0 ) { + i = max; + + } else { + i = one ? index : 0; + } + + // Loop through all the selected options + for ( ; i < max; i++ ) { + option = options[ i ]; + + // Support: IE <=9 only + // IE8-9 doesn't update selected after form reset (#2551) + if ( ( option.selected || i === index ) && + + // Don't return options that are disabled or in a disabled optgroup + !option.disabled && + ( !option.parentNode.disabled || + !nodeName( option.parentNode, "optgroup" ) ) ) { + + // Get the specific value for the option + value = jQuery( option ).val(); + + // We don't need an array for one selects + if ( one ) { + return value; + } + + // Multi-Selects return an array + values.push( value ); + } + } + + return values; + }, + + set: function( elem, value ) { + var optionSet, option, + options = elem.options, + values = jQuery.makeArray( value ), + i = options.length; + + while ( i-- ) { + option = options[ i ]; + + /* eslint-disable no-cond-assign */ + + if ( option.selected = + jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1 + ) { + optionSet = true; + } + + /* eslint-enable no-cond-assign */ + } + + // Force browsers to behave consistently when non-matching value is set + if ( !optionSet ) { + elem.selectedIndex = -1; + } + return values; + } + } + } +} ); + +// Radios and checkboxes getter/setter +jQuery.each( [ "radio", "checkbox" ], function() { + jQuery.valHooks[ this ] = { + set: function( elem, value ) { + if ( Array.isArray( value ) ) { + return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 ); + } + } + }; + if ( !support.checkOn ) { + jQuery.valHooks[ this ].get = function( elem ) { + return elem.getAttribute( "value" ) === null ? "on" : elem.value; + }; + } +} ); + + + + +// Return jQuery for attributes-only inclusion + + +support.focusin = "onfocusin" in window; + + +var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, + stopPropagationCallback = function( e ) { + e.stopPropagation(); + }; + +jQuery.extend( jQuery.event, { + + trigger: function( event, data, elem, onlyHandlers ) { + + var i, cur, tmp, bubbleType, ontype, handle, special, lastElement, + eventPath = [ elem || document ], + type = hasOwn.call( event, "type" ) ? event.type : event, + namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : []; + + cur = lastElement = tmp = elem = elem || document; + + // Don't do events on text and comment nodes + if ( elem.nodeType === 3 || elem.nodeType === 8 ) { + return; + } + + // focus/blur morphs to focusin/out; ensure we're not firing them right now + if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { + return; + } + + if ( type.indexOf( "." ) > -1 ) { + + // Namespaced trigger; create a regexp to match event type in handle() + namespaces = type.split( "." ); + type = namespaces.shift(); + namespaces.sort(); + } + ontype = type.indexOf( ":" ) < 0 && "on" + type; + + // Caller can pass in a jQuery.Event object, Object, or just an event type string + event = event[ jQuery.expando ] ? + event : + new jQuery.Event( type, typeof event === "object" && event ); + + // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) + event.isTrigger = onlyHandlers ? 2 : 3; + event.namespace = namespaces.join( "." ); + event.rnamespace = event.namespace ? + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) : + null; + + // Clean up the event in case it is being reused + event.result = undefined; + if ( !event.target ) { + event.target = elem; + } + + // Clone any incoming data and prepend the event, creating the handler arg list + data = data == null ? + [ event ] : + jQuery.makeArray( data, [ event ] ); + + // Allow special events to draw outside the lines + special = jQuery.event.special[ type ] || {}; + if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) { + return; + } + + // Determine event propagation path in advance, per W3C events spec (#9951) + // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) + if ( !onlyHandlers && !special.noBubble && !isWindow( elem ) ) { + + bubbleType = special.delegateType || type; + if ( !rfocusMorph.test( bubbleType + type ) ) { + cur = cur.parentNode; + } + for ( ; cur; cur = cur.parentNode ) { + eventPath.push( cur ); + tmp = cur; + } + + // Only add window if we got to document (e.g., not plain obj or detached DOM) + if ( tmp === ( elem.ownerDocument || document ) ) { + eventPath.push( tmp.defaultView || tmp.parentWindow || window ); + } + } + + // Fire handlers on the event path + i = 0; + while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) { + lastElement = cur; + event.type = i > 1 ? + bubbleType : + special.bindType || type; + + // jQuery handler + handle = ( dataPriv.get( cur, "events" ) || Object.create( null ) )[ event.type ] && + dataPriv.get( cur, "handle" ); + if ( handle ) { + handle.apply( cur, data ); + } + + // Native handler + handle = ontype && cur[ ontype ]; + if ( handle && handle.apply && acceptData( cur ) ) { + event.result = handle.apply( cur, data ); + if ( event.result === false ) { + event.preventDefault(); + } + } + } + event.type = type; + + // If nobody prevented the default action, do it now + if ( !onlyHandlers && !event.isDefaultPrevented() ) { + + if ( ( !special._default || + special._default.apply( eventPath.pop(), data ) === false ) && + acceptData( elem ) ) { + + // Call a native DOM method on the target with the same name as the event. + // Don't do default actions on window, that's where global variables be (#6170) + if ( ontype && isFunction( elem[ type ] ) && !isWindow( elem ) ) { + + // Don't re-trigger an onFOO event when we call its FOO() method + tmp = elem[ ontype ]; + + if ( tmp ) { + elem[ ontype ] = null; + } + + // Prevent re-triggering of the same event, since we already bubbled it above + jQuery.event.triggered = type; + + if ( event.isPropagationStopped() ) { + lastElement.addEventListener( type, stopPropagationCallback ); + } + + elem[ type ](); + + if ( event.isPropagationStopped() ) { + lastElement.removeEventListener( type, stopPropagationCallback ); + } + + jQuery.event.triggered = undefined; + + if ( tmp ) { + elem[ ontype ] = tmp; + } + } + } + } + + return event.result; + }, + + // Piggyback on a donor event to simulate a different one + // Used only for `focus(in | out)` events + simulate: function( type, elem, event ) { + var e = jQuery.extend( + new jQuery.Event(), + event, + { + type: type, + isSimulated: true + } + ); + + jQuery.event.trigger( e, null, elem ); + } + +} ); + +jQuery.fn.extend( { + + trigger: function( type, data ) { + return this.each( function() { + jQuery.event.trigger( type, data, this ); + } ); + }, + triggerHandler: function( type, data ) { + var elem = this[ 0 ]; + if ( elem ) { + return jQuery.event.trigger( type, data, elem, true ); + } + } +} ); + + +// Support: Firefox <=44 +// Firefox doesn't have focus(in | out) events +// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787 +// +// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1 +// focus(in | out) events fire after focus & blur events, +// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order +// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857 +if ( !support.focusin ) { + jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) { + + // Attach a single capturing handler on the document while someone wants focusin/focusout + var handler = function( event ) { + jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) ); + }; + + jQuery.event.special[ fix ] = { + setup: function() { + + // Handle: regular nodes (via `this.ownerDocument`), window + // (via `this.document`) & document (via `this`). + var doc = this.ownerDocument || this.document || this, + attaches = dataPriv.access( doc, fix ); + + if ( !attaches ) { + doc.addEventListener( orig, handler, true ); + } + dataPriv.access( doc, fix, ( attaches || 0 ) + 1 ); + }, + teardown: function() { + var doc = this.ownerDocument || this.document || this, + attaches = dataPriv.access( doc, fix ) - 1; + + if ( !attaches ) { + doc.removeEventListener( orig, handler, true ); + dataPriv.remove( doc, fix ); + + } else { + dataPriv.access( doc, fix, attaches ); + } + } + }; + } ); +} +var location = window.location; + +var nonce = { guid: Date.now() }; + +var rquery = ( /\?/ ); + + + +// Cross-browser xml parsing +jQuery.parseXML = function( data ) { + var xml, parserErrorElem; + if ( !data || typeof data !== "string" ) { + return null; + } + + // Support: IE 9 - 11 only + // IE throws on parseFromString with invalid input. + try { + xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" ); + } catch ( e ) {} + + parserErrorElem = xml && xml.getElementsByTagName( "parsererror" )[ 0 ]; + if ( !xml || parserErrorElem ) { + jQuery.error( "Invalid XML: " + ( + parserErrorElem ? + jQuery.map( parserErrorElem.childNodes, function( el ) { + return el.textContent; + } ).join( "\n" ) : + data + ) ); + } + return xml; +}; + + +var + rbracket = /\[\]$/, + rCRLF = /\r?\n/g, + rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i, + rsubmittable = /^(?:input|select|textarea|keygen)/i; + +function buildParams( prefix, obj, traditional, add ) { + var name; + + if ( Array.isArray( obj ) ) { + + // Serialize array item. + jQuery.each( obj, function( i, v ) { + if ( traditional || rbracket.test( prefix ) ) { + + // Treat each array item as a scalar. + add( prefix, v ); + + } else { + + // Item is non-scalar (array or object), encode its numeric index. + buildParams( + prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]", + v, + traditional, + add + ); + } + } ); + + } else if ( !traditional && toType( obj ) === "object" ) { + + // Serialize object item. + for ( name in obj ) { + buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); + } + + } else { + + // Serialize scalar item. + add( prefix, obj ); + } +} + +// Serialize an array of form elements or a set of +// key/values into a query string +jQuery.param = function( a, traditional ) { + var prefix, + s = [], + add = function( key, valueOrFunction ) { + + // If value is a function, invoke it and use its return value + var value = isFunction( valueOrFunction ) ? + valueOrFunction() : + valueOrFunction; + + s[ s.length ] = encodeURIComponent( key ) + "=" + + encodeURIComponent( value == null ? "" : value ); + }; + + if ( a == null ) { + return ""; + } + + // If an array was passed in, assume that it is an array of form elements. + if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { + + // Serialize the form elements + jQuery.each( a, function() { + add( this.name, this.value ); + } ); + + } else { + + // If traditional, encode the "old" way (the way 1.3.2 or older + // did it), otherwise encode params recursively. + for ( prefix in a ) { + buildParams( prefix, a[ prefix ], traditional, add ); + } + } + + // Return the resulting serialization + return s.join( "&" ); +}; + +jQuery.fn.extend( { + serialize: function() { + return jQuery.param( this.serializeArray() ); + }, + serializeArray: function() { + return this.map( function() { + + // Can add propHook for "elements" to filter or add form elements + var elements = jQuery.prop( this, "elements" ); + return elements ? jQuery.makeArray( elements ) : this; + } ).filter( function() { + var type = this.type; + + // Use .is( ":disabled" ) so that fieldset[disabled] works + return this.name && !jQuery( this ).is( ":disabled" ) && + rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) && + ( this.checked || !rcheckableType.test( type ) ); + } ).map( function( _i, elem ) { + var val = jQuery( this ).val(); + + if ( val == null ) { + return null; + } + + if ( Array.isArray( val ) ) { + return jQuery.map( val, function( val ) { + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ); + } + + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ).get(); + } +} ); + + +var + r20 = /%20/g, + rhash = /#.*$/, + rantiCache = /([?&])_=[^&]*/, + rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg, + + // #7653, #8125, #8152: local protocol detection + rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/, + rnoContent = /^(?:GET|HEAD)$/, + rprotocol = /^\/\//, + + /* Prefilters + * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example) + * 2) These are called: + * - BEFORE asking for a transport + * - AFTER param serialization (s.data is a string if s.processData is true) + * 3) key is the dataType + * 4) the catchall symbol "*" can be used + * 5) execution will start with transport dataType and THEN continue down to "*" if needed + */ + prefilters = {}, + + /* Transports bindings + * 1) key is the dataType + * 2) the catchall symbol "*" can be used + * 3) selection will start with transport dataType and THEN go to "*" if needed + */ + transports = {}, + + // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression + allTypes = "*/".concat( "*" ), + + // Anchor tag for parsing the document origin + originAnchor = document.createElement( "a" ); + +originAnchor.href = location.href; + +// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport +function addToPrefiltersOrTransports( structure ) { + + // dataTypeExpression is optional and defaults to "*" + return function( dataTypeExpression, func ) { + + if ( typeof dataTypeExpression !== "string" ) { + func = dataTypeExpression; + dataTypeExpression = "*"; + } + + var dataType, + i = 0, + dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || []; + + if ( isFunction( func ) ) { + + // For each dataType in the dataTypeExpression + while ( ( dataType = dataTypes[ i++ ] ) ) { + + // Prepend if requested + if ( dataType[ 0 ] === "+" ) { + dataType = dataType.slice( 1 ) || "*"; + ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func ); + + // Otherwise append + } else { + ( structure[ dataType ] = structure[ dataType ] || [] ).push( func ); + } + } + } + }; +} + +// Base inspection function for prefilters and transports +function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) { + + var inspected = {}, + seekingTransport = ( structure === transports ); + + function inspect( dataType ) { + var selected; + inspected[ dataType ] = true; + jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) { + var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR ); + if ( typeof dataTypeOrTransport === "string" && + !seekingTransport && !inspected[ dataTypeOrTransport ] ) { + + options.dataTypes.unshift( dataTypeOrTransport ); + inspect( dataTypeOrTransport ); + return false; + } else if ( seekingTransport ) { + return !( selected = dataTypeOrTransport ); + } + } ); + return selected; + } + + return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" ); +} + +// A special extend for ajax options +// that takes "flat" options (not to be deep extended) +// Fixes #9887 +function ajaxExtend( target, src ) { + var key, deep, + flatOptions = jQuery.ajaxSettings.flatOptions || {}; + + for ( key in src ) { + if ( src[ key ] !== undefined ) { + ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ]; + } + } + if ( deep ) { + jQuery.extend( true, target, deep ); + } + + return target; +} + +/* Handles responses to an ajax request: + * - finds the right dataType (mediates between content-type and expected dataType) + * - returns the corresponding response + */ +function ajaxHandleResponses( s, jqXHR, responses ) { + + var ct, type, finalDataType, firstDataType, + contents = s.contents, + dataTypes = s.dataTypes; + + // Remove auto dataType and get content-type in the process + while ( dataTypes[ 0 ] === "*" ) { + dataTypes.shift(); + if ( ct === undefined ) { + ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" ); + } + } + + // Check if we're dealing with a known content-type + if ( ct ) { + for ( type in contents ) { + if ( contents[ type ] && contents[ type ].test( ct ) ) { + dataTypes.unshift( type ); + break; + } + } + } + + // Check to see if we have a response for the expected dataType + if ( dataTypes[ 0 ] in responses ) { + finalDataType = dataTypes[ 0 ]; + } else { + + // Try convertible dataTypes + for ( type in responses ) { + if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) { + finalDataType = type; + break; + } + if ( !firstDataType ) { + firstDataType = type; + } + } + + // Or just use first one + finalDataType = finalDataType || firstDataType; + } + + // If we found a dataType + // We add the dataType to the list if needed + // and return the corresponding response + if ( finalDataType ) { + if ( finalDataType !== dataTypes[ 0 ] ) { + dataTypes.unshift( finalDataType ); + } + return responses[ finalDataType ]; + } +} + +/* Chain conversions given the request and the original response + * Also sets the responseXXX fields on the jqXHR instance + */ +function ajaxConvert( s, response, jqXHR, isSuccess ) { + var conv2, current, conv, tmp, prev, + converters = {}, + + // Work with a copy of dataTypes in case we need to modify it for conversion + dataTypes = s.dataTypes.slice(); + + // Create converters map with lowercased keys + if ( dataTypes[ 1 ] ) { + for ( conv in s.converters ) { + converters[ conv.toLowerCase() ] = s.converters[ conv ]; + } + } + + current = dataTypes.shift(); + + // Convert to each sequential dataType + while ( current ) { + + if ( s.responseFields[ current ] ) { + jqXHR[ s.responseFields[ current ] ] = response; + } + + // Apply the dataFilter if provided + if ( !prev && isSuccess && s.dataFilter ) { + response = s.dataFilter( response, s.dataType ); + } + + prev = current; + current = dataTypes.shift(); + + if ( current ) { + + // There's only work to do if current dataType is non-auto + if ( current === "*" ) { + + current = prev; + + // Convert response if prev dataType is non-auto and differs from current + } else if ( prev !== "*" && prev !== current ) { + + // Seek a direct converter + conv = converters[ prev + " " + current ] || converters[ "* " + current ]; + + // If none found, seek a pair + if ( !conv ) { + for ( conv2 in converters ) { + + // If conv2 outputs current + tmp = conv2.split( " " ); + if ( tmp[ 1 ] === current ) { + + // If prev can be converted to accepted input + conv = converters[ prev + " " + tmp[ 0 ] ] || + converters[ "* " + tmp[ 0 ] ]; + if ( conv ) { + + // Condense equivalence converters + if ( conv === true ) { + conv = converters[ conv2 ]; + + // Otherwise, insert the intermediate dataType + } else if ( converters[ conv2 ] !== true ) { + current = tmp[ 0 ]; + dataTypes.unshift( tmp[ 1 ] ); + } + break; + } + } + } + } + + // Apply converter (if not an equivalence) + if ( conv !== true ) { + + // Unless errors are allowed to bubble, catch and return them + if ( conv && s.throws ) { + response = conv( response ); + } else { + try { + response = conv( response ); + } catch ( e ) { + return { + state: "parsererror", + error: conv ? e : "No conversion from " + prev + " to " + current + }; + } + } + } + } + } + } + + return { state: "success", data: response }; +} + +jQuery.extend( { + + // Counter for holding the number of active queries + active: 0, + + // Last-Modified header cache for next request + lastModified: {}, + etag: {}, + + ajaxSettings: { + url: location.href, + type: "GET", + isLocal: rlocalProtocol.test( location.protocol ), + global: true, + processData: true, + async: true, + contentType: "application/x-www-form-urlencoded; charset=UTF-8", + + /* + timeout: 0, + data: null, + dataType: null, + username: null, + password: null, + cache: null, + throws: false, + traditional: false, + headers: {}, + */ + + accepts: { + "*": allTypes, + text: "text/plain", + html: "text/html", + xml: "application/xml, text/xml", + json: "application/json, text/javascript" + }, + + contents: { + xml: /\bxml\b/, + html: /\bhtml/, + json: /\bjson\b/ + }, + + responseFields: { + xml: "responseXML", + text: "responseText", + json: "responseJSON" + }, + + // Data converters + // Keys separate source (or catchall "*") and destination types with a single space + converters: { + + // Convert anything to text + "* text": String, + + // Text to html (true = no transformation) + "text html": true, + + // Evaluate text as a json expression + "text json": JSON.parse, + + // Parse text as xml + "text xml": jQuery.parseXML + }, + + // For options that shouldn't be deep extended: + // you can add your own custom options here if + // and when you create one that shouldn't be + // deep extended (see ajaxExtend) + flatOptions: { + url: true, + context: true + } + }, + + // Creates a full fledged settings object into target + // with both ajaxSettings and settings fields. + // If target is omitted, writes into ajaxSettings. + ajaxSetup: function( target, settings ) { + return settings ? + + // Building a settings object + ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) : + + // Extending ajaxSettings + ajaxExtend( jQuery.ajaxSettings, target ); + }, + + ajaxPrefilter: addToPrefiltersOrTransports( prefilters ), + ajaxTransport: addToPrefiltersOrTransports( transports ), + + // Main method + ajax: function( url, options ) { + + // If url is an object, simulate pre-1.5 signature + if ( typeof url === "object" ) { + options = url; + url = undefined; + } + + // Force options to be an object + options = options || {}; + + var transport, + + // URL without anti-cache param + cacheURL, + + // Response headers + responseHeadersString, + responseHeaders, + + // timeout handle + timeoutTimer, + + // Url cleanup var + urlAnchor, + + // Request state (becomes false upon send and true upon completion) + completed, + + // To know if global events are to be dispatched + fireGlobals, + + // Loop variable + i, + + // uncached part of the url + uncached, + + // Create the final options object + s = jQuery.ajaxSetup( {}, options ), + + // Callbacks context + callbackContext = s.context || s, + + // Context for global events is callbackContext if it is a DOM node or jQuery collection + globalEventContext = s.context && + ( callbackContext.nodeType || callbackContext.jquery ) ? + jQuery( callbackContext ) : + jQuery.event, + + // Deferreds + deferred = jQuery.Deferred(), + completeDeferred = jQuery.Callbacks( "once memory" ), + + // Status-dependent callbacks + statusCode = s.statusCode || {}, + + // Headers (they are sent all at once) + requestHeaders = {}, + requestHeadersNames = {}, + + // Default abort message + strAbort = "canceled", + + // Fake xhr + jqXHR = { + readyState: 0, + + // Builds headers hashtable if needed + getResponseHeader: function( key ) { + var match; + if ( completed ) { + if ( !responseHeaders ) { + responseHeaders = {}; + while ( ( match = rheaders.exec( responseHeadersString ) ) ) { + responseHeaders[ match[ 1 ].toLowerCase() + " " ] = + ( responseHeaders[ match[ 1 ].toLowerCase() + " " ] || [] ) + .concat( match[ 2 ] ); + } + } + match = responseHeaders[ key.toLowerCase() + " " ]; + } + return match == null ? null : match.join( ", " ); + }, + + // Raw string + getAllResponseHeaders: function() { + return completed ? responseHeadersString : null; + }, + + // Caches the header + setRequestHeader: function( name, value ) { + if ( completed == null ) { + name = requestHeadersNames[ name.toLowerCase() ] = + requestHeadersNames[ name.toLowerCase() ] || name; + requestHeaders[ name ] = value; + } + return this; + }, + + // Overrides response content-type header + overrideMimeType: function( type ) { + if ( completed == null ) { + s.mimeType = type; + } + return this; + }, + + // Status-dependent callbacks + statusCode: function( map ) { + var code; + if ( map ) { + if ( completed ) { + + // Execute the appropriate callbacks + jqXHR.always( map[ jqXHR.status ] ); + } else { + + // Lazy-add the new callbacks in a way that preserves old ones + for ( code in map ) { + statusCode[ code ] = [ statusCode[ code ], map[ code ] ]; + } + } + } + return this; + }, + + // Cancel the request + abort: function( statusText ) { + var finalText = statusText || strAbort; + if ( transport ) { + transport.abort( finalText ); + } + done( 0, finalText ); + return this; + } + }; + + // Attach deferreds + deferred.promise( jqXHR ); + + // Add protocol if not provided (prefilters might expect it) + // Handle falsy url in the settings object (#10093: consistency with old signature) + // We also use the url parameter if available + s.url = ( ( url || s.url || location.href ) + "" ) + .replace( rprotocol, location.protocol + "//" ); + + // Alias method option to type as per ticket #12004 + s.type = options.method || options.type || s.method || s.type; + + // Extract dataTypes list + s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ]; + + // A cross-domain request is in order when the origin doesn't match the current origin. + if ( s.crossDomain == null ) { + urlAnchor = document.createElement( "a" ); + + // Support: IE <=8 - 11, Edge 12 - 15 + // IE throws exception on accessing the href property if url is malformed, + // e.g. http://example.com:80x/ + try { + urlAnchor.href = s.url; + + // Support: IE <=8 - 11 only + // Anchor's host property isn't correctly set when s.url is relative + urlAnchor.href = urlAnchor.href; + s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !== + urlAnchor.protocol + "//" + urlAnchor.host; + } catch ( e ) { + + // If there is an error parsing the URL, assume it is crossDomain, + // it can be rejected by the transport if it is invalid + s.crossDomain = true; + } + } + + // Convert data if not already a string + if ( s.data && s.processData && typeof s.data !== "string" ) { + s.data = jQuery.param( s.data, s.traditional ); + } + + // Apply prefilters + inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); + + // If request was aborted inside a prefilter, stop there + if ( completed ) { + return jqXHR; + } + + // We can fire global events as of now if asked to + // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118) + fireGlobals = jQuery.event && s.global; + + // Watch for a new set of requests + if ( fireGlobals && jQuery.active++ === 0 ) { + jQuery.event.trigger( "ajaxStart" ); + } + + // Uppercase the type + s.type = s.type.toUpperCase(); + + // Determine if request has content + s.hasContent = !rnoContent.test( s.type ); + + // Save the URL in case we're toying with the If-Modified-Since + // and/or If-None-Match header later on + // Remove hash to simplify url manipulation + cacheURL = s.url.replace( rhash, "" ); + + // More options handling for requests with no content + if ( !s.hasContent ) { + + // Remember the hash so we can put it back + uncached = s.url.slice( cacheURL.length ); + + // If data is available and should be processed, append data to url + if ( s.data && ( s.processData || typeof s.data === "string" ) ) { + cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data; + + // #9682: remove data so that it's not used in an eventual retry + delete s.data; + } + + // Add or update anti-cache param if needed + if ( s.cache === false ) { + cacheURL = cacheURL.replace( rantiCache, "$1" ); + uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce.guid++ ) + + uncached; + } + + // Put hash and anti-cache on the URL that will be requested (gh-1732) + s.url = cacheURL + uncached; + + // Change '%20' to '+' if this is encoded form body content (gh-2658) + } else if ( s.data && s.processData && + ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) { + s.data = s.data.replace( r20, "+" ); + } + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + if ( jQuery.lastModified[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] ); + } + if ( jQuery.etag[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] ); + } + } + + // Set the correct header, if data is being sent + if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { + jqXHR.setRequestHeader( "Content-Type", s.contentType ); + } + + // Set the Accepts header for the server, depending on the dataType + jqXHR.setRequestHeader( + "Accept", + s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ? + s.accepts[ s.dataTypes[ 0 ] ] + + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) : + s.accepts[ "*" ] + ); + + // Check for headers option + for ( i in s.headers ) { + jqXHR.setRequestHeader( i, s.headers[ i ] ); + } + + // Allow custom headers/mimetypes and early abort + if ( s.beforeSend && + ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) { + + // Abort if not done already and return + return jqXHR.abort(); + } + + // Aborting is no longer a cancellation + strAbort = "abort"; + + // Install callbacks on deferreds + completeDeferred.add( s.complete ); + jqXHR.done( s.success ); + jqXHR.fail( s.error ); + + // Get transport + transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); + + // If no transport, we auto-abort + if ( !transport ) { + done( -1, "No Transport" ); + } else { + jqXHR.readyState = 1; + + // Send global event + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); + } + + // If request was aborted inside ajaxSend, stop there + if ( completed ) { + return jqXHR; + } + + // Timeout + if ( s.async && s.timeout > 0 ) { + timeoutTimer = window.setTimeout( function() { + jqXHR.abort( "timeout" ); + }, s.timeout ); + } + + try { + completed = false; + transport.send( requestHeaders, done ); + } catch ( e ) { + + // Rethrow post-completion exceptions + if ( completed ) { + throw e; + } + + // Propagate others as results + done( -1, e ); + } + } + + // Callback for when everything is done + function done( status, nativeStatusText, responses, headers ) { + var isSuccess, success, error, response, modified, + statusText = nativeStatusText; + + // Ignore repeat invocations + if ( completed ) { + return; + } + + completed = true; + + // Clear timeout if it exists + if ( timeoutTimer ) { + window.clearTimeout( timeoutTimer ); + } + + // Dereference transport for early garbage collection + // (no matter how long the jqXHR object will be used) + transport = undefined; + + // Cache response headers + responseHeadersString = headers || ""; + + // Set readyState + jqXHR.readyState = status > 0 ? 4 : 0; + + // Determine if successful + isSuccess = status >= 200 && status < 300 || status === 304; + + // Get response data + if ( responses ) { + response = ajaxHandleResponses( s, jqXHR, responses ); + } + + // Use a noop converter for missing script but not if jsonp + if ( !isSuccess && + jQuery.inArray( "script", s.dataTypes ) > -1 && + jQuery.inArray( "json", s.dataTypes ) < 0 ) { + s.converters[ "text script" ] = function() {}; + } + + // Convert no matter what (that way responseXXX fields are always set) + response = ajaxConvert( s, response, jqXHR, isSuccess ); + + // If successful, handle type chaining + if ( isSuccess ) { + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + modified = jqXHR.getResponseHeader( "Last-Modified" ); + if ( modified ) { + jQuery.lastModified[ cacheURL ] = modified; + } + modified = jqXHR.getResponseHeader( "etag" ); + if ( modified ) { + jQuery.etag[ cacheURL ] = modified; + } + } + + // if no content + if ( status === 204 || s.type === "HEAD" ) { + statusText = "nocontent"; + + // if not modified + } else if ( status === 304 ) { + statusText = "notmodified"; + + // If we have data, let's convert it + } else { + statusText = response.state; + success = response.data; + error = response.error; + isSuccess = !error; + } + } else { + + // Extract error from statusText and normalize for non-aborts + error = statusText; + if ( status || !statusText ) { + statusText = "error"; + if ( status < 0 ) { + status = 0; + } + } + } + + // Set data for the fake xhr object + jqXHR.status = status; + jqXHR.statusText = ( nativeStatusText || statusText ) + ""; + + // Success/Error + if ( isSuccess ) { + deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); + } else { + deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); + } + + // Status-dependent callbacks + jqXHR.statusCode( statusCode ); + statusCode = undefined; + + if ( fireGlobals ) { + globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError", + [ jqXHR, s, isSuccess ? success : error ] ); + } + + // Complete + completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] ); + + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] ); + + // Handle the global AJAX counter + if ( !( --jQuery.active ) ) { + jQuery.event.trigger( "ajaxStop" ); + } + } + } + + return jqXHR; + }, + + getJSON: function( url, data, callback ) { + return jQuery.get( url, data, callback, "json" ); + }, + + getScript: function( url, callback ) { + return jQuery.get( url, undefined, callback, "script" ); + } +} ); + +jQuery.each( [ "get", "post" ], function( _i, method ) { + jQuery[ method ] = function( url, data, callback, type ) { + + // Shift arguments if data argument was omitted + if ( isFunction( data ) ) { + type = type || callback; + callback = data; + data = undefined; + } + + // The url can be an options object (which then must have .url) + return jQuery.ajax( jQuery.extend( { + url: url, + type: method, + dataType: type, + data: data, + success: callback + }, jQuery.isPlainObject( url ) && url ) ); + }; +} ); + +jQuery.ajaxPrefilter( function( s ) { + var i; + for ( i in s.headers ) { + if ( i.toLowerCase() === "content-type" ) { + s.contentType = s.headers[ i ] || ""; + } + } +} ); + + +jQuery._evalUrl = function( url, options, doc ) { + return jQuery.ajax( { + url: url, + + // Make this explicit, since user can override this through ajaxSetup (#11264) + type: "GET", + dataType: "script", + cache: true, + async: false, + global: false, + + // Only evaluate the response if it is successful (gh-4126) + // dataFilter is not invoked for failure responses, so using it instead + // of the default converter is kludgy but it works. + converters: { + "text script": function() {} + }, + dataFilter: function( response ) { + jQuery.globalEval( response, options, doc ); + } + } ); +}; + + +jQuery.fn.extend( { + wrapAll: function( html ) { + var wrap; + + if ( this[ 0 ] ) { + if ( isFunction( html ) ) { + html = html.call( this[ 0 ] ); + } + + // The elements to wrap the target around + wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true ); + + if ( this[ 0 ].parentNode ) { + wrap.insertBefore( this[ 0 ] ); + } + + wrap.map( function() { + var elem = this; + + while ( elem.firstElementChild ) { + elem = elem.firstElementChild; + } + + return elem; + } ).append( this ); + } + + return this; + }, + + wrapInner: function( html ) { + if ( isFunction( html ) ) { + return this.each( function( i ) { + jQuery( this ).wrapInner( html.call( this, i ) ); + } ); + } + + return this.each( function() { + var self = jQuery( this ), + contents = self.contents(); + + if ( contents.length ) { + contents.wrapAll( html ); + + } else { + self.append( html ); + } + } ); + }, + + wrap: function( html ) { + var htmlIsFunction = isFunction( html ); + + return this.each( function( i ) { + jQuery( this ).wrapAll( htmlIsFunction ? html.call( this, i ) : html ); + } ); + }, + + unwrap: function( selector ) { + this.parent( selector ).not( "body" ).each( function() { + jQuery( this ).replaceWith( this.childNodes ); + } ); + return this; + } +} ); + + +jQuery.expr.pseudos.hidden = function( elem ) { + return !jQuery.expr.pseudos.visible( elem ); +}; +jQuery.expr.pseudos.visible = function( elem ) { + return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length ); +}; + + + + +jQuery.ajaxSettings.xhr = function() { + try { + return new window.XMLHttpRequest(); + } catch ( e ) {} +}; + +var xhrSuccessStatus = { + + // File protocol always yields status code 0, assume 200 + 0: 200, + + // Support: IE <=9 only + // #1450: sometimes IE returns 1223 when it should be 204 + 1223: 204 + }, + xhrSupported = jQuery.ajaxSettings.xhr(); + +support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported ); +support.ajax = xhrSupported = !!xhrSupported; + +jQuery.ajaxTransport( function( options ) { + var callback, errorCallback; + + // Cross domain only allowed if supported through XMLHttpRequest + if ( support.cors || xhrSupported && !options.crossDomain ) { + return { + send: function( headers, complete ) { + var i, + xhr = options.xhr(); + + xhr.open( + options.type, + options.url, + options.async, + options.username, + options.password + ); + + // Apply custom fields if provided + if ( options.xhrFields ) { + for ( i in options.xhrFields ) { + xhr[ i ] = options.xhrFields[ i ]; + } + } + + // Override mime type if needed + if ( options.mimeType && xhr.overrideMimeType ) { + xhr.overrideMimeType( options.mimeType ); + } + + // X-Requested-With header + // For cross-domain requests, seeing as conditions for a preflight are + // akin to a jigsaw puzzle, we simply never set it to be sure. + // (it can always be set on a per-request basis or even using ajaxSetup) + // For same-domain requests, won't change header if already provided. + if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) { + headers[ "X-Requested-With" ] = "XMLHttpRequest"; + } + + // Set headers + for ( i in headers ) { + xhr.setRequestHeader( i, headers[ i ] ); + } + + // Callback + callback = function( type ) { + return function() { + if ( callback ) { + callback = errorCallback = xhr.onload = + xhr.onerror = xhr.onabort = xhr.ontimeout = + xhr.onreadystatechange = null; + + if ( type === "abort" ) { + xhr.abort(); + } else if ( type === "error" ) { + + // Support: IE <=9 only + // On a manual native abort, IE9 throws + // errors on any property access that is not readyState + if ( typeof xhr.status !== "number" ) { + complete( 0, "error" ); + } else { + complete( + + // File: protocol always yields status 0; see #8605, #14207 + xhr.status, + xhr.statusText + ); + } + } else { + complete( + xhrSuccessStatus[ xhr.status ] || xhr.status, + xhr.statusText, + + // Support: IE <=9 only + // IE9 has no XHR2 but throws on binary (trac-11426) + // For XHR2 non-text, let the caller handle it (gh-2498) + ( xhr.responseType || "text" ) !== "text" || + typeof xhr.responseText !== "string" ? + { binary: xhr.response } : + { text: xhr.responseText }, + xhr.getAllResponseHeaders() + ); + } + } + }; + }; + + // Listen to events + xhr.onload = callback(); + errorCallback = xhr.onerror = xhr.ontimeout = callback( "error" ); + + // Support: IE 9 only + // Use onreadystatechange to replace onabort + // to handle uncaught aborts + if ( xhr.onabort !== undefined ) { + xhr.onabort = errorCallback; + } else { + xhr.onreadystatechange = function() { + + // Check readyState before timeout as it changes + if ( xhr.readyState === 4 ) { + + // Allow onerror to be called first, + // but that will not handle a native abort + // Also, save errorCallback to a variable + // as xhr.onerror cannot be accessed + window.setTimeout( function() { + if ( callback ) { + errorCallback(); + } + } ); + } + }; + } + + // Create the abort callback + callback = callback( "abort" ); + + try { + + // Do send the request (this may raise an exception) + xhr.send( options.hasContent && options.data || null ); + } catch ( e ) { + + // #14683: Only rethrow if this hasn't been notified as an error yet + if ( callback ) { + throw e; + } + } + }, + + abort: function() { + if ( callback ) { + callback(); + } + } + }; + } +} ); + + + + +// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432) +jQuery.ajaxPrefilter( function( s ) { + if ( s.crossDomain ) { + s.contents.script = false; + } +} ); + +// Install script dataType +jQuery.ajaxSetup( { + accepts: { + script: "text/javascript, application/javascript, " + + "application/ecmascript, application/x-ecmascript" + }, + contents: { + script: /\b(?:java|ecma)script\b/ + }, + converters: { + "text script": function( text ) { + jQuery.globalEval( text ); + return text; + } + } +} ); + +// Handle cache's special case and crossDomain +jQuery.ajaxPrefilter( "script", function( s ) { + if ( s.cache === undefined ) { + s.cache = false; + } + if ( s.crossDomain ) { + s.type = "GET"; + } +} ); + +// Bind script tag hack transport +jQuery.ajaxTransport( "script", function( s ) { + + // This transport only deals with cross domain or forced-by-attrs requests + if ( s.crossDomain || s.scriptAttrs ) { + var script, callback; + return { + send: function( _, complete ) { + script = jQuery( " - - - - - - - + + + + + + + - - - -
    -
    -
    -
    +
    +
    +
    +
    @@ -109,18 +65,18 @@

    Software For The Integration Of Multi-Omics Experiments In Bioconductor

    https://doi.org/10.1158/0008-5472.CAN-17-0344

    - - +

    BioC status Platforms codecov Downloads

    Installation

    We recommend installing the stable release version of MultiAssayExperiment in Bioconductor. This can be done using BiocManager:

    -
    -if (!require("BiocManager", quietly = TRUE))
    +
    if (!require("BiocManager"))
         install.packages("BiocManager")
     
    -BiocManager::install("MultiAssayExperiment")
    +library(BiocManager) + +install("MultiAssayExperiment")

    Schematic @@ -135,11 +91,7 @@

    Schematic -MultiAssayExperiment schematic

    -MultiAssayExperiment schematic -

    -

    +

    MultiAssayExperiment schematic

    Cheatsheet @@ -150,20 +102,18 @@

    CheatsheetReady-to-use MultiAssayExperiment objects

    For easy-to-use and ready-made MultiAssayExperiment objects, use the curatedTCGAData experiment data package.

    -
    -BiocManager::install("curatedTCGAData")
    +
    install("curatedTCGAData")

    Companion package for working with TCGA data

    TCGAutils is a handy package for working with MultiAssayExperiment data objects from curatedTCGAData. It is highly recommended to use TCGAutils for identifier manipulation, sample identification and more.

    -
    -BiocManager::install("TCGAutils")
    +
    install("TCGAutils")

    Documentation

    -

    The MultiAssayExperiment API is available by browsing to the API wiki.

    +

    The MultiAssayExperiment API is available by browsing to the API wiki.

    The MultiAssayExperiment Bioconductor Special Interest Group @@ -178,18 +128,15 @@

    Contributor Code of Conduct, version 1.0.0, available at http://contributor-covenant.org/version/1/0/0/

    +

    This Code of Conduct is adapted from the Contributor Covenant, version 1.0.0, available at http://contributor-covenant.org/version/1/0/0/

    -
    - - + +
    -
    - - + diff --git a/katex-auto.js b/katex-auto.js new file mode 100644 index 00000000..20651d9f --- /dev/null +++ b/katex-auto.js @@ -0,0 +1,14 @@ +// https://github.com/jgm/pandoc/blob/29fa97ab96b8e2d62d48326e1b949a71dc41f47a/src/Text/Pandoc/Writers/HTML.hs#L332-L345 +document.addEventListener("DOMContentLoaded", function () { + var mathElements = document.getElementsByClassName("math"); + var macros = []; + for (var i = 0; i < mathElements.length; i++) { + var texText = mathElements[i].firstChild; + if (mathElements[i].tagName == "SPAN") { + katex.render(texText.data, mathElements[i], { + displayMode: mathElements[i].classList.contains("display"), + throwOnError: false, + macros: macros, + fleqn: false + }); + }}}); diff --git a/lightswitch.js b/lightswitch.js new file mode 100644 index 00000000..9467125a --- /dev/null +++ b/lightswitch.js @@ -0,0 +1,85 @@ + +/*! + * Color mode toggler for Bootstrap's docs (https://getbootstrap.com/) + * Copyright 2011-2023 The Bootstrap Authors + * Licensed under the Creative Commons Attribution 3.0 Unported License. + * Updates for {pkgdown} by the {bslib} authors, also licensed under CC-BY-3.0. + */ + +const getStoredTheme = () => localStorage.getItem('theme') +const setStoredTheme = theme => localStorage.setItem('theme', theme) + +const getPreferredTheme = () => { + const storedTheme = getStoredTheme() + if (storedTheme) { + return storedTheme + } + + return window.matchMedia('(prefers-color-scheme: dark)').matches ? 'dark' : 'light' +} + +const setTheme = theme => { + if (theme === 'auto') { + document.documentElement.setAttribute('data-bs-theme', (window.matchMedia('(prefers-color-scheme: dark)').matches ? 'dark' : 'light')) + } else { + document.documentElement.setAttribute('data-bs-theme', theme) + } +} + +function bsSetupThemeToggle () { + 'use strict' + + const showActiveTheme = (theme, focus = false) => { + var activeLabel, activeIcon; + + document.querySelectorAll('[data-bs-theme-value]').forEach(element => { + const buttonTheme = element.getAttribute('data-bs-theme-value') + const isActive = buttonTheme == theme + + element.classList.toggle('active', isActive) + element.setAttribute('aria-pressed', isActive) + + if (isActive) { + activeLabel = element.textContent; + activeIcon = element.querySelector('span').classList.value; + } + }) + + const themeSwitcher = document.querySelector('#dropdown-lightswitch') + if (!themeSwitcher) { + return + } + + themeSwitcher.setAttribute('aria-label', activeLabel) + themeSwitcher.querySelector('span').classList.value = activeIcon; + + if (focus) { + themeSwitcher.focus() + } + } + + window.matchMedia('(prefers-color-scheme: dark)').addEventListener('change', () => { + const storedTheme = getStoredTheme() + if (storedTheme !== 'light' && storedTheme !== 'dark') { + setTheme(getPreferredTheme()) + } + }) + + window.addEventListener('DOMContentLoaded', () => { + showActiveTheme(getPreferredTheme()) + + document + .querySelectorAll('[data-bs-theme-value]') + .forEach(toggle => { + toggle.addEventListener('click', () => { + const theme = toggle.getAttribute('data-bs-theme-value') + setTheme(theme) + setStoredTheme(theme) + showActiveTheme(theme, true) + }) + }) + }) +} + +setTheme(getPreferredTheme()); +bsSetupThemeToggle(); diff --git a/news/index.html b/news/index.html index bccbc5d3..0ca8ef89 100644 --- a/news/index.html +++ b/news/index.html @@ -1,83 +1,61 @@ -Changelog • MultiAssayExperiment - +Changelog • MultiAssayExperiment + Skip to contents -
    -
    -
    - +
    +
    +
    - +

    Changes in version 1.30.3

    +
    +

    Bug fixes and minor improvements

    +
    • The colData<- replacement method now correctly works with data.frame value inputs (@drighelli, #330).
    • +
    • Updated CITATION information in the main vignette.
    • +
    • Use reshape2::melt instead of stats::reshape to preserve row names in longFormat +
    • +
    • When rownames are numeric characters e.g., “1”, ensure they stay character when converting MultiAssayExperiment to longFormat.
    • +
    +
    +
    +

    Changes in version 1.28.0

    New features

    -
    • Dropped experiments are no longer kept in the metadata slot. They can be seen with drops() (@LTLA, #323).
    • +
      • Dropped experiments are no longer kept in the metadata slot. They can be seen with drops() (@LTLA, #323).

    Bug fixes and minor improvements

    @@ -85,22 +63,22 @@

    Bug fixes and minor improvement

    - +

    Changes in version 1.26.0

    New features

    • showReplicated displays the actual colnames of technical replicates by assay and biological unit.
    • -
    • The bracket replacement method [<- for MultiAssayExperiment now also replaces the names with those from the right-hand side of the operation, if any (@DarioS, #319)
    • +
    • The bracket replacement method [<- for MultiAssayExperiment now also replaces the names with those from the right-hand side of the operation, if any (@DarioS, #319)

    Bug fixes and minor improvements

    -
    • During single assay replacement [[<-, the re-ordering of assays based on the value input was invalid when empty assays present (@danielinteractive, #322).
    • +
      • During single assay replacement [[<-, the re-ordering of assays based on the value input was invalid when empty assays present (@danielinteractive, #322).
      • Permuting assays also updates the order of names in the MultiAssayExperiment and assays in the sampleMap
    - +

    Changes in version 1.24.0

    New features

    • @@ -111,19 +89,19 @@

      New featuresBug fixes and minor improvements

      • Added an assay<- replacement method for robustifying saveHDF5MultiAssayExperiment with plain matrices
      • Use BiocBaseUtils::setSlots and avoid warnings of triple colon use.
      • -
      • Resolve issue when colData has one column when merging two MultiAssayExperiment objects, i.e., using the c method (@cvanderaa, #315)
      • -
      • Increase efficiency in colnames and rownames methods (@cvanderaa, #314)
      • -
      • Make ‘prefix’ inputs consistent in saveHDF5MultiAssayExperiment and loadHDF5MultiAssayExperiment (@asiyeka, #313)
      • +
      • Resolve issue when colData has one column when merging two MultiAssayExperiment objects, i.e., using the c method (@cvanderaa, #315)
      • +
      • Increase efficiency in colnames and rownames methods (@cvanderaa, #314)
      • +
      • Make ‘prefix’ inputs consistent in saveHDF5MultiAssayExperiment and loadHDF5MultiAssayExperiment (@asiyeka, #313)
      • Improve performance for replicated method
      • -
      • Update wideFormat documentation, when replicates present additional sets of columns will be appended to the produced DataFrame (@DarioS, #312)
      • +
      • Update wideFormat documentation, when replicates present additional sets of columns will be appended to the produced DataFrame (@DarioS, #312)
    - +

    Changes in version 1.22.0

    Bug fixes and minor improvements

    • Add data("miniACC") to examples after removing lazy loading.
    • -
    • Class definition prototypes defined for cleaner extensibility (@hpages, #306).
    • +
    • Class definition prototypes defined for cleaner extensibility (@hpages, #306).
    • Doc and internal improvments to MultiAssayExperimentToMAF
    • @@ -132,15 +110,15 @@

      Bug fixes and minor improvement

    - +

    Changes in version 1.20.0

    Bug fixes and minor improvements

    -
    • Avoid dropping experiments with repeated calls to subsetByColData and remove harmonization (@cvanderaa, #302)
    • +
      • Avoid dropping experiments with repeated calls to subsetByColData and remove harmonization (@cvanderaa, #302)
      • -getWithColData suppresses messages from natural subsetting operations by default with verbose = FALSE (@bhagwataditya, #301)
      • +getWithColData suppresses messages from natural subsetting operations by default with verbose = FALSE (@bhagwataditya, #301)
      • -getWithColData was using the old default (drop = TRUE) and causing an error when the experiment is empty (@danielinteractive, #300).
      • -
      • Calls to the internal .harmonize operation are reduced to increase memory efficiency, when identical experiment colnames present (@LTLA, #299).
      • +getWithColData was using the old default (drop = TRUE) and causing an error when the experiment is empty (@danielinteractive, #300). +
      • Calls to the internal .harmonize operation are reduced to increase memory efficiency, when identical experiment colnames present (@LTLA, #299).
      • subsetByColData now errors on subscript vectors longer than the nrow of the colData (previously a warning).
      • @@ -149,7 +127,7 @@

        Bug fixes and minor improvement

    - +

    Changes in version 1.18.0

    New features

    • @@ -171,14 +149,14 @@

      New features

    Bug fixes and minor improvements

    -
    • Updated the constructor function to auto-populate rownames in colData when it is missing (@LTLA, #287)
    • +
      • Updated the constructor function to auto-populate rownames in colData when it is missing (@LTLA, #287)
      • The metadata now includes names of dropped experiments
      • Updated validity checks to support array-like classes
      • Dropped experiments are tracked in the metadata
    - +

    Changes in version 1.16.0

    New features

    • Coercion methods from list/List to MultiAssayExperiment method now available.
    • @@ -187,51 +165,51 @@

      New featuresBug fixes and minor improvements

      • Provide more details in documentation for mergeReplicates
      • -
      • Improved documentation for accessor function return values, helper function examples (@llrs, #281)
      • -
      • Fixed bug when using longFormat with character assay matrices (@jonocarroll, #282)
      • +
      • Improved documentation for accessor function return values, helper function examples (@llrs, #281)
      • +
      • Fixed bug when using longFormat with character assay matrices (@jonocarroll, #282)
    - +

    Changes in version 1.14.0

    New features

    • exportClass creates a number of .csv data files for exporting data
    • -
    • Allow vector input i for selecting assays in longFormat (@lgatto, #266)
    • +
    • Allow vector input i for selecting assays in longFormat (@lgatto, #266)
    • Updates to ‘Using MultiAssayExperiment with DelayedMatrix’ vignette

    Bug fixes and minor improvements

    -
    • Warn when colData rownames and ExperimentList colnames are empty (@LTLA #262)
    • -
    • Add informative error message for ExperimentList (@lgatto, #265)
    • +
      • Warn when colData rownames and ExperimentList colnames are empty (@LTLA #262)
      • +
      • Add informative error message for ExperimentList (@lgatto, #265)
      • Informative warning when dropping ExperimentList element columns (@lwaldron)
      • -
      • Fixes to constructor functions, MultiAssayExperiment and MatchedAssayExperiment (@lgatto, #267 #268, @lwaldron)
      • +
      • Fixes to constructor functions, MultiAssayExperiment and MatchedAssayExperiment (@lgatto, #267 #268, @lwaldron)
      • Add warning when j in mae[i, j, k] is longer than colData rows
      • Strict argument matching between generic and methods
      • Updates due to class(matrix())
      • -UpsetSamples more robust to differences in names between split sampleMap and names(ExperimentList) (@jonocarroll, #269)
      • +UpsetSamples more robust to differences in names between split sampleMap and names(ExperimentList) (@jonocarroll, #269)
      • Refactored and improved UpsetSamples
      • -ExperimentList propagation of mcols and metadata (@vobencha, #270)
      • -
      • Enforcement of validObject with replacement methods colData and sampleMap (@vobencha, #271)
      • +ExperimentList propagation of mcols and metadata (@vobencha, #270) +
      • Enforcement of validObject with replacement methods colData and sampleMap (@vobencha, #271)
    - +

    Changes in version 1.12.0

    Bug fixes and minor improvements

    -
    • Improvements to the main vignette, MultiAssayExperiment class schematic now included (@mtmorgan, #261)
    • +
      • Improvements to the main vignette, MultiAssayExperiment class schematic now included (@mtmorgan, #261)
      • Updated documentation for the upsetSamples function
      • Update code to use splitAsList from S4Vectors (@hpages)
      • -
      • Fixed bug with metadata disappearing from ExperimentList when replacing it inside a MultiAssayExperiment object (@lawremi, #259)
      • +
      • Fixed bug with metadata disappearing from ExperimentList when replacing it inside a MultiAssayExperiment object (@lawremi, #259)
      • Fixed the formatting of the NEWS file
    - +

    Changes in version 1.10.0

    New features

    • @@ -252,7 +230,7 @@

      Bug fixes and minor improvement

    - +

    Changes in version 1.8.0

    New features

    • The single bracket replacement method [<- added to support assignment of assay datasets
    • @@ -284,11 +262,11 @@

      Bug fixes and minor improvements

    - +

    Changes in version 1.6.0

    New features

    • -DataFrame now exported for users (@DarioS, #242)
    • +DataFrame now exported for users (@DarioS, #242)
    • c is smarter at matching colnames with primary names and creating a sampleMap
    • @@ -327,7 +305,7 @@

      Bug fixes and minor improvements
    • Minor vignette changes
    • Supply a collapse character for wideFormat column names
    • -upsetSamples does not munge experiment names with special characters when check.names = FALSE (by default keeps hyphens, underscores, etc.). A nameFilter functional argument allows operations such as substr on the experiment names. (@vjcitn, #231)
    • +upsetSamples does not munge experiment names with special characters when check.names = FALSE (by default keeps hyphens, underscores, etc.). A nameFilter functional argument allows operations such as substr on the experiment names. (@vjcitn, #231)
    • Updates to prepMultiAssay
    • Enhancements to the main vignette
    • @@ -341,7 +319,7 @@

      Bug fixes and minor improvements

    - +

    Changes in version 1.1.59

    New features

    • @@ -359,7 +337,7 @@

      Bug fixes and minor improvement

    - +

    Changes in version 1.1.52

    New features

    • @@ -370,7 +348,7 @@

      New features

    - +

    Changes in version 1.1.49

    New features

    • @@ -387,14 +365,14 @@

      Bug fixes and minor improvement

    - +

    Changes in version 1.1.44

    Bug fixes and minor improvements

    • Renamed PrepMultiAssay to prepMultiAssay (lower p following convention)
    - +

    Changes in version 1.1.43

    New features

    • The MultiAssayExperiment quickstart guide vignette added
    • @@ -422,7 +400,7 @@

      Bug fixes and minor improvement

    - +

    Changes in version 1.1.37

    New features

    • @@ -444,7 +422,7 @@

      Bug fixes and minor improvement

    - +

    Changes in version 1.1.27

    New features

    • @@ -469,7 +447,7 @@

      Bug fixes and minor improvement

    - +

    Changes in version 1.1.17

    New features

    • @@ -477,7 +455,7 @@

      New features

    - +

    Changes in version 1.1.16

    New features

    • Implement shape argument for rearrange function: wide now available
    • @@ -488,7 +466,7 @@

      Bug fixes and minor improvement

    - +

    Changes in version 1.1.15

    New features

    • @@ -505,7 +483,7 @@

      Bug fixes and minor improvement

    - +

    Changes in version 1.1.12

    New features

    • @@ -516,7 +494,7 @@

      New features

    - +

    Changes in version 1.1.11

    New features

    • Renamed gather function to collect @@ -524,14 +502,14 @@

      New features

    - +

    Changes in version 1.1.10

    New features

    • Double bracket method for MultiAssayExperiment available
    - +

    Changes in version 1.1.9

    New features

    • @@ -543,7 +521,7 @@

      Bug fixes and minor improvements

    - +

    Changes in version 1.1.6

    New features

    • Added an example HNSC dataset
    • @@ -559,7 +537,7 @@

      Bug fixes and minor improvements

    - +

    Changes in version 1.1.2

    New features

    • @@ -577,7 +555,7 @@

      Bug fixes and minor improvements

    - +

    Changes in version 1.1.1

    New features

    @@ -652,29 +630,23 @@

    Bug fixes and minor improvements mapToList preserves list order

    -
    +
    - +
    - -
    -
    - - diff --git a/pkgdown.css b/pkgdown.css deleted file mode 100644 index 80ea5b83..00000000 --- a/pkgdown.css +++ /dev/null @@ -1,384 +0,0 @@ -/* Sticky footer */ - -/** - * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/ - * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css - * - * .Site -> body > .container - * .Site-content -> body > .container .row - * .footer -> footer - * - * Key idea seems to be to ensure that .container and __all its parents__ - * have height set to 100% - * - */ - -html, body { - height: 100%; -} - -body { - position: relative; -} - -body > .container { - display: flex; - height: 100%; - flex-direction: column; -} - -body > .container .row { - flex: 1 0 auto; -} - -footer { - margin-top: 45px; - padding: 35px 0 36px; - border-top: 1px solid #e5e5e5; - color: #666; - display: flex; - flex-shrink: 0; -} -footer p { - margin-bottom: 0; -} -footer div { - flex: 1; -} -footer .pkgdown { - text-align: right; -} -footer p { - margin-bottom: 0; -} - -img.icon { - float: right; -} - -/* Ensure in-page images don't run outside their container */ -.contents img { - max-width: 100%; - height: auto; -} - -/* Fix bug in bootstrap (only seen in firefox) */ -summary { - display: list-item; -} - -/* Typographic tweaking ---------------------------------*/ - -.contents .page-header { - margin-top: calc(-60px + 1em); -} - -dd { - margin-left: 3em; -} - -/* Section anchors ---------------------------------*/ - -a.anchor { - display: none; - margin-left: 5px; - width: 20px; - height: 20px; - - background-image: url(./link.svg); - background-repeat: no-repeat; - background-size: 20px 20px; - background-position: center center; -} - -h1:hover .anchor, -h2:hover .anchor, -h3:hover .anchor, -h4:hover .anchor, -h5:hover .anchor, -h6:hover .anchor { - display: inline-block; -} - -/* Fixes for fixed navbar --------------------------*/ - -.contents h1, .contents h2, .contents h3, .contents h4 { - padding-top: 60px; - margin-top: -40px; -} - -/* Navbar submenu --------------------------*/ - -.dropdown-submenu { - position: relative; -} - -.dropdown-submenu>.dropdown-menu { - top: 0; - left: 100%; - margin-top: -6px; - margin-left: -1px; - border-radius: 0 6px 6px 6px; -} - -.dropdown-submenu:hover>.dropdown-menu { - display: block; -} - -.dropdown-submenu>a:after { - display: block; - content: " "; - float: right; - width: 0; - height: 0; - border-color: transparent; - border-style: solid; - border-width: 5px 0 5px 5px; - border-left-color: #cccccc; - margin-top: 5px; - margin-right: -10px; -} - -.dropdown-submenu:hover>a:after { - border-left-color: #ffffff; -} - -.dropdown-submenu.pull-left { - float: none; -} - -.dropdown-submenu.pull-left>.dropdown-menu { - left: -100%; - margin-left: 10px; - border-radius: 6px 0 6px 6px; -} - -/* Sidebar --------------------------*/ - -#pkgdown-sidebar { - margin-top: 30px; - position: -webkit-sticky; - position: sticky; - top: 70px; -} - -#pkgdown-sidebar h2 { - font-size: 1.5em; - margin-top: 1em; -} - -#pkgdown-sidebar h2:first-child { - margin-top: 0; -} - -#pkgdown-sidebar .list-unstyled li { - margin-bottom: 0.5em; -} - -/* bootstrap-toc tweaks ------------------------------------------------------*/ - -/* All levels of nav */ - -nav[data-toggle='toc'] .nav > li > a { - padding: 4px 20px 4px 6px; - font-size: 1.5rem; - font-weight: 400; - color: inherit; -} - -nav[data-toggle='toc'] .nav > li > a:hover, -nav[data-toggle='toc'] .nav > li > a:focus { - padding-left: 5px; - color: inherit; - border-left: 1px solid #878787; -} - -nav[data-toggle='toc'] .nav > .active > a, -nav[data-toggle='toc'] .nav > .active:hover > a, -nav[data-toggle='toc'] .nav > .active:focus > a { - padding-left: 5px; - font-size: 1.5rem; - font-weight: 400; - color: inherit; - border-left: 2px solid #878787; -} - -/* Nav: second level (shown on .active) */ - -nav[data-toggle='toc'] .nav .nav { - display: none; /* Hide by default, but at >768px, show it */ - padding-bottom: 10px; -} - -nav[data-toggle='toc'] .nav .nav > li > a { - padding-left: 16px; - font-size: 1.35rem; -} - -nav[data-toggle='toc'] .nav .nav > li > a:hover, -nav[data-toggle='toc'] .nav .nav > li > a:focus { - padding-left: 15px; -} - -nav[data-toggle='toc'] .nav .nav > .active > a, -nav[data-toggle='toc'] .nav .nav > .active:hover > a, -nav[data-toggle='toc'] .nav .nav > .active:focus > a { - padding-left: 15px; - font-weight: 500; - font-size: 1.35rem; -} - -/* orcid ------------------------------------------------------------------- */ - -.orcid { - font-size: 16px; - color: #A6CE39; - /* margins are required by official ORCID trademark and display guidelines */ - margin-left:4px; - margin-right:4px; - vertical-align: middle; -} - -/* Reference index & topics ----------------------------------------------- */ - -.ref-index th {font-weight: normal;} - -.ref-index td {vertical-align: top; min-width: 100px} -.ref-index .icon {width: 40px;} -.ref-index .alias {width: 40%;} -.ref-index-icons .alias {width: calc(40% - 40px);} -.ref-index .title {width: 60%;} - -.ref-arguments th {text-align: right; padding-right: 10px;} -.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px} -.ref-arguments .name {width: 20%;} -.ref-arguments .desc {width: 80%;} - -/* Nice scrolling for wide elements --------------------------------------- */ - -table { - display: block; - overflow: auto; -} - -/* Syntax highlighting ---------------------------------------------------- */ - -pre, code, pre code { - background-color: #f8f8f8; - color: #333; -} -pre, pre code { - white-space: pre-wrap; - word-break: break-all; - overflow-wrap: break-word; -} - -pre { - border: 1px solid #eee; -} - -pre .img, pre .r-plt { - margin: 5px 0; -} - -pre .img img, pre .r-plt img { - background-color: #fff; -} - -code a, pre a { - color: #375f84; -} - -a.sourceLine:hover { - text-decoration: none; -} - -.fl {color: #1514b5;} -.fu {color: #000000;} /* function */ -.ch,.st {color: #036a07;} /* string */ -.kw {color: #264D66;} /* keyword */ -.co {color: #888888;} /* comment */ - -.error {font-weight: bolder;} -.warning {font-weight: bolder;} - -/* Clipboard --------------------------*/ - -.hasCopyButton { - position: relative; -} - -.btn-copy-ex { - position: absolute; - right: 0; - top: 0; - visibility: hidden; -} - -.hasCopyButton:hover button.btn-copy-ex { - visibility: visible; -} - -/* headroom.js ------------------------ */ - -.headroom { - will-change: transform; - transition: transform 200ms linear; -} -.headroom--pinned { - transform: translateY(0%); -} -.headroom--unpinned { - transform: translateY(-100%); -} - -/* mark.js ----------------------------*/ - -mark { - background-color: rgba(255, 255, 51, 0.5); - border-bottom: 2px solid rgba(255, 153, 51, 0.3); - padding: 1px; -} - -/* vertical spacing after htmlwidgets */ -.html-widget { - margin-bottom: 10px; -} - -/* fontawesome ------------------------ */ - -.fab { - font-family: "Font Awesome 5 Brands" !important; -} - -/* don't display links in code chunks when printing */ -/* source: https://stackoverflow.com/a/10781533 */ -@media print { - code a:link:after, code a:visited:after { - content: ""; - } -} - -/* Section anchors --------------------------------- - Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71 -*/ - -div.csl-bib-body { } -div.csl-entry { - clear: both; -} -.hanging-indent div.csl-entry { - margin-left:2em; - text-indent:-2em; -} -div.csl-left-margin { - min-width:2em; - float:left; -} -div.csl-right-inline { - margin-left:2em; - padding-left:1em; -} -div.csl-indent { - margin-left: 2em; -} diff --git a/pkgdown.js b/pkgdown.js index 6f0eee40..9757bf9e 100644 --- a/pkgdown.js +++ b/pkgdown.js @@ -2,83 +2,43 @@ (function($) { $(function() { - $('.navbar-fixed-top').headroom(); + $('nav.navbar').headroom(); - $('body').css('padding-top', $('.navbar').height() + 10); - $(window).resize(function(){ - $('body').css('padding-top', $('.navbar').height() + 10); + Toc.init({ + $nav: $("#toc"), + $scope: $("main h2, main h3, main h4, main h5, main h6") }); - $('[data-toggle="tooltip"]').tooltip(); - - var cur_path = paths(location.pathname); - var links = $("#navbar ul li a"); - var max_length = -1; - var pos = -1; - for (var i = 0; i < links.length; i++) { - if (links[i].getAttribute("href") === "#") - continue; - // Ignore external links - if (links[i].host !== location.host) - continue; - - var nav_path = paths(links[i].pathname); - - var length = prefix_length(nav_path, cur_path); - if (length > max_length) { - max_length = length; - pos = i; - } - } - - // Add class to parent
  • , and enclosing
  • if in dropdown - if (pos >= 0) { - var menu_anchor = $(links[pos]); - menu_anchor.parent().addClass("active"); - menu_anchor.closest("li.dropdown").addClass("active"); - } - }); - - function paths(pathname) { - var pieces = pathname.split("/"); - pieces.shift(); // always starts with / - - var end = pieces[pieces.length - 1]; - if (end === "index.html" || end === "") - pieces.pop(); - return(pieces); - } - - // Returns -1 if not found - function prefix_length(needle, haystack) { - if (needle.length > haystack.length) - return(-1); - - // Special case for length-0 haystack, since for loop won't run - if (haystack.length === 0) { - return(needle.length === 0 ? 0 : -1); + if ($('#toc').length) { + $('body').scrollspy({ + target: '#toc', + offset: $("nav.navbar").outerHeight() + 1 + }); } - for (var i = 0; i < haystack.length; i++) { - if (needle[i] != haystack[i]) - return(i); - } + // Activate popovers + $('[data-bs-toggle="popover"]').popover({ + container: 'body', + html: true, + trigger: 'focus', + placement: "top", + sanitize: false, + }); - return(haystack.length); - } + $('[data-bs-toggle="tooltip"]').tooltip(); /* Clipboard --------------------------*/ function changeTooltipMessage(element, msg) { - var tooltipOriginalTitle=element.getAttribute('data-original-title'); - element.setAttribute('data-original-title', msg); + var tooltipOriginalTitle=element.getAttribute('data-bs-original-title'); + element.setAttribute('data-bs-original-title', msg); $(element).tooltip('show'); - element.setAttribute('data-original-title', tooltipOriginalTitle); + element.setAttribute('data-bs-original-title', tooltipOriginalTitle); } if(ClipboardJS.isSupported()) { $(document).ready(function() { - var copyButton = ""; + var copyButton = ""; $("div.sourceCode").addClass("hasCopyButton"); @@ -89,20 +49,106 @@ $('.btn-copy-ex').tooltip({container: 'body'}); // Initialize clipboard: - var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { + var clipboard = new ClipboardJS('[data-clipboard-copy]', { text: function(trigger) { return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, ""); } }); - clipboardBtnCopies.on('success', function(e) { + clipboard.on('success', function(e) { changeTooltipMessage(e.trigger, 'Copied!'); e.clearSelection(); }); - clipboardBtnCopies.on('error', function() { + clipboard.on('error', function(e) { changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); }); + }); } + + /* Search marking --------------------------*/ + var url = new URL(window.location.href); + var toMark = url.searchParams.get("q"); + var mark = new Mark("main#main"); + if (toMark) { + mark.mark(toMark, { + accuracy: { + value: "complementary", + limiters: [",", ".", ":", "/"], + } + }); + } + + /* Search --------------------------*/ + /* Adapted from https://github.com/rstudio/bookdown/blob/2d692ba4b61f1e466c92e78fd712b0ab08c11d31/inst/resources/bs4_book/bs4_book.js#L25 */ + // Initialise search index on focus + var fuse; + $("#search-input").focus(async function(e) { + if (fuse) { + return; + } + + $(e.target).addClass("loading"); + var response = await fetch($("#search-input").data("search-index")); + var data = await response.json(); + + var options = { + keys: ["what", "text", "code"], + ignoreLocation: true, + threshold: 0.1, + includeMatches: true, + includeScore: true, + }; + fuse = new Fuse(data, options); + + $(e.target).removeClass("loading"); + }); + + // Use algolia autocomplete + var options = { + autoselect: true, + debug: true, + hint: false, + minLength: 2, + }; + var q; +async function searchFuse(query, callback) { + await fuse; + + var items; + if (!fuse) { + items = []; + } else { + q = query; + var results = fuse.search(query, { limit: 20 }); + items = results + .filter((x) => x.score <= 0.75) + .map((x) => x.item); + if (items.length === 0) { + items = [{dir:"Sorry 😿",previous_headings:"",title:"No results found.",what:"No results found.",path:window.location.href}]; + } + } + callback(items); +} + $("#search-input").autocomplete(options, [ + { + name: "content", + source: searchFuse, + templates: { + suggestion: (s) => { + if (s.title == s.what) { + return `${s.dir} >
    ${s.title}
    `; + } else if (s.previous_headings == "") { + return `${s.dir} >
    ${s.title}
    > ${s.what}`; + } else { + return `${s.dir} >
    ${s.title}
    > ${s.previous_headings} > ${s.what}`; + } + }, + }, + }, + ]).on('autocomplete:selected', function(event, s) { + window.location.href = s.path + "?q=" + q + "#" + s.id; + }); + }); })(window.jQuery || window.$) diff --git a/pkgdown.yml b/pkgdown.yml index 4cc8cbfa..b56d0949 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,10 +1,12 @@ -pandoc: 3.1.1 -pkgdown: 2.0.7 +pandoc: '3.2' +pkgdown: 2.1.0 pkgdown_sha: ~ articles: + extras/MAE-curatedMetagenomicData: extras/MAE-curatedMetagenomicData.html MultiAssayExperiment: MultiAssayExperiment.html QuickStartMultiAssay: QuickStartMultiAssay.html UsingHDF5Array: UsingHDF5Array.html - MAE-curatedMetagenomicData: extras/MAE-curatedMetagenomicData.html -last_built: 2024-01-24T22:51Z - +last_built: 2024-08-14T16:05Z +urls: + reference: https://github.com/waldronlab/MultiAssayExperiment/reference + article: https://github.com/waldronlab/MultiAssayExperiment/articles diff --git a/reference/$,MultiAssayExperiment-method.html b/reference/$,MultiAssayExperiment-method.html new file mode 100644 index 00000000..71716772 --- /dev/null +++ b/reference/$,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/DataFrame.html b/reference/DataFrame.html new file mode 100644 index 00000000..934aa03e --- /dev/null +++ b/reference/DataFrame.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/ExperimentList-class.html b/reference/ExperimentList-class.html index 0ab7dbc7..f85b1c09 100644 --- a/reference/ExperimentList-class.html +++ b/reference/ExperimentList-class.html @@ -1,177 +1,151 @@ -ExperimentList - A container for multi-experiment data — ExperimentList-class • MultiAssayExperimentExperimentList - A container for multi-experiment data — ExperimentList-class • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    The ExperimentList class is a container that builds on - the SimpleList with additional checks for consistency in experiment - names and length. It contains a SimpleList of experiments with - sample identifiers. One element present per experiment performed.

    +the SimpleList with additional checks for consistency in experiment +names and length. It contains a SimpleList of experiments with +sample identifiers. One element present per experiment performed.

    Convert from SimpleList or list to the multi-experiment data - container. When using the mergeReplicates method, additional - arguments are passed to the given simplify function argument (e.g., - na.rm = TRUE)

    +container. When using the mergeReplicates method, additional +arguments are passed to the given simplify function argument (e.g., +na.rm = TRUE)

    -
    -
    # S4 method for ExperimentList
    +    
    +

    Usage

    +
    # S4 method for class 'ExperimentList'
     show(object)
     
    -# S4 method for ExperimentList
    +# S4 method for class 'ExperimentList'
     isEmpty(x)
     
    -# S4 method for ExperimentList
    +# S4 method for class 'ExperimentList'
     dimnames(x)
     
    -# S4 method for ExperimentList
    +# S4 method for class 'ExperimentList'
     colnames(x, do.NULL = TRUE, prefix = "col")
     
    -# S4 method for ExperimentList
    +# S4 method for class 'ExperimentList'
     rownames(x, do.NULL = TRUE, prefix = "row")
     
    -# S4 method for ExperimentList
    +# S4 method for class 'ExperimentList'
     mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...)
     
    -# S4 method for ANY,missing
    +# S4 method for class 'ANY,missing'
     assay(x, i, withDimnames = TRUE, ...)
     
    -# S4 method for ExperimentList
    +# S4 method for class 'ExperimentList'
     assays(x, withDimnames = TRUE, ...)
     
    -# S4 method for ExperimentList,missing
    +# S4 method for class 'ExperimentList,missing'
     assay(x, i, withDimnames = TRUE, ...)
     
    -# S4 method for ExperimentList,numeric
    +# S4 method for class 'ExperimentList,numeric'
     assay(x, i, withDimnames = TRUE, ...)
     
    -# S4 method for ExperimentList,character
    +# S4 method for class 'ExperimentList,character'
     assay(x, i, withDimnames = TRUE, ...)
    -
    -

    Arguments

    -
    object, x
    -

    An ExperimentList object

    +
    +

    Arguments

    + +
    object, x
    +

    An ExperimentList object

    -
    do.NULL, prefix
    + +
    do.NULL, prefix

    See ?base::rownames for a description of these arguments.

    -
    replicates
    -

    mergeReplicates: A list or LogicalList +

    replicates
    +

    mergeReplicates: A list or LogicalList where each element represents a sample and a vector of repeated measurements for the sample

    -
    simplify
    +
    simplify

    A function for merging columns where duplicates are indicated by replicates

    -
    ...
    +
    ...

    Additional arguments. See details for more information.

    -
    i
    +
    i

    A scalar character or integer index

    -
    withDimnames
    +
    withDimnames

    logical (default TRUE) whether to return dimension names

    -
    -

    Value

    - - -

    An ExperimentList class object

    +
    +

    Value

    +

    An ExperimentList class object

    -
    -

    Methods (by generic)

    - -
    • show(ExperimentList): Show method for -ExperimentList class

    • +
      +

      Methods (by generic)

      + +
      • show(ExperimentList): Show method for ExperimentList class

      • isEmpty(ExperimentList): check for zero length across all experiments

      • dimnames(ExperimentList): Get the dimension names for @@ -185,22 +159,22 @@

        Methods (by generic)

      • assay(x = ANY, i = missing): Obtain the specified assay with a numeric or character reference

      • assays(ExperimentList): Get the assay data from each element in the -ExperimentList

      • +ExperimentList

      -
      -

      coercion

      - +
      +

      coercion

      +

      Convert a list or S4 List to an ExperimentList using the as() function.

      In the following example, x is either a list or -List:

      -
          \code{as(x, "ExperimentList")}
      +List:

      +
          as(x, "ExperimentList")
      -
      -

      Examples

      +
      +

      Examples

      
       ExperimentList()
       #> ExperimentList class object of length 0:
      @@ -208,27 +182,23 @@ 

      Examples

      -
      - -
      +
    -
    +
    + - - diff --git a/reference/ExperimentList.html b/reference/ExperimentList.html index 11ed9480..d1c33032 100644 --- a/reference/ExperimentList.html +++ b/reference/ExperimentList.html @@ -1,108 +1,79 @@ -Represent multiple experiments as a List-derivative ExperimentList — ExperimentList • MultiAssayExperimentRepresent multiple experiments as a List-derivative ExperimentList — ExperimentList • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    The ExperimentList class can contain several different types of data. The only requirements for an ExperimentList class are that the objects contained have the following set of methods: dim, [, dimnames

    -
    +
    +

    Usage

    ExperimentList(...)
    -
    -

    Arguments

    -
    ...
    +
    +

    Arguments

    + + +
    ...

    A named list class object

    -
    -

    Value

    - - -

    A ExperimentList class object of experiment data

    +
    +

    Value

    +

    A ExperimentList class object of experiment data

    -
    -

    Examples

    +
    +

    Examples

    ## Create an empty ExperimentList instance
     ExperimentList()
     #> ExperimentList class object of length 0:
    @@ -158,27 +129,23 @@ 

    Examples

    ExpList <- ExperimentList(assayList)
    -
    - -
    +
    -
    +
    + - - diff --git a/reference/HDF5MultiAssayExperiment.html b/reference/HDF5MultiAssayExperiment.html index abbb6092..3f3e2002 100644 --- a/reference/HDF5MultiAssayExperiment.html +++ b/reference/HDF5MultiAssayExperiment.html @@ -1,5 +1,5 @@ -Save a MultiAssayExperiment class object to HDF5 and Rds files — saveHDF5MultiAssayExperiment • MultiAssayExperimentSave a MultiAssayExperiment class object to HDF5 and Rds files — saveHDF5MultiAssayExperiment • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    This function takes a MultiAssayExperiment object and uses the assays functionality to obtain data matrices out of the experiments. These are then saved into the .h5 file format. This function relies heavily on the HDF5Array package whose installation is required before use. saveHDF5MultiAssayExpeirment preserves the classes contained in the -ExperimentList with the exception of matrix which is +ExperimentList with the exception of matrix which is converted to HDF5Matrix. Internal SummarizedExperiment assays are converted to HDF5-backed assays as in HDF5Array::saveHDF5SummarizedExperiment. SummarizedExperiment @@ -104,7 +84,8 @@

    Save a MultiAssayExperiment class object to HDF5 and Rds files

    HDF5-backed MultiAssayExperiment.

    -
    +
    +

    Usage

    saveHDF5MultiAssayExperiment(
       x,
       dir = "h5_mae",
    @@ -119,22 +100,24 @@ 

    Save a MultiAssayExperiment class object to HDF5 and Rds files

    loadHDF5MultiAssayExperiment(dir = "h5_mae", prefix = NULL)
    -
    -

    Arguments

    -
    x
    -

    A MultiAssayExperiment object or derivative

    +
    +

    Arguments

    + + +
    x
    +

    A MultiAssayExperiment object or derivative

    -
    dir
    +
    dir

    The path (as a single string) to the directory where to save the -HDF5-based MultiAssayExperiment object or to load it from.

    +HDF5-based MultiAssayExperiment object or to load it from.

    When saving, the directory will be created if it doesn't already exist. If the directory already exists and no prefix is specified and replace is set to TRUE, then it's replaced with an empty directory.

    -
    prefix
    +
    prefix

    An optional prefix to add to the names of the files created inside dir. This allows saving more than one object in the same directory. When the prefix is NULL, the name of the x input @@ -144,20 +127,20 @@

    Arguments

    words, e.g., "test".

    -
    replace
    +
    replace

    When no prefix is specified, should a pre-existing directory be replaced with a new empty one? The content of the pre-existing directory will be lost!

    -
    chunkdim, level
    +
    chunkdim, level

    The dimensions of the chunks and the compression level to use for writing the assay data to disk.

    Passed to the internal calls to writeHDF5Array. See ?writeHDF5Array for more information.

    -
    as.sparse
    +
    as.sparse

    Whether the assay data should be flagged as sparse or not. If set to NA (the default), then the specific as.sparse value to use for each assay is determined by calling is_sparse() on them.

    @@ -166,7 +149,7 @@

    Arguments

    IMPORTANT NOTE.

    -
    verbose
    +
    verbose

    Set to TRUE to make the function display progress.

    In the case of saveHDF5MultiAssayExperiment(), verbose is set to NA by default, in which case verbosity is controlled @@ -175,8 +158,8 @@

    Arguments

    -
    -

    Examples

    +
    +

    Examples

    
     data("miniACC")
     
    @@ -186,47 +169,47 @@ 

    Examples

    miniACC, dir = testDir, verbose = TRUE, replace = TRUE ) #> Start writing assay 1/5 to HDF5 file: -#> /tmp/RtmpswreTL/test_mae/miniACC_experiments.h5 -#> / Reading and realizing block 1/1 ... -#> OK +#> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 +#> / reading and realizing block 1/1 ... +#> ok #> \ Writing it ... #> OK #> Finished writing assay 1/5 to HDF5 file: -#> /tmp/RtmpswreTL/test_mae/miniACC_experiments.h5 +#> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> Start writing assay 2/5 to HDF5 file: -#> /tmp/RtmpswreTL/test_mae/miniACC_experiments.h5 -#> / Reading and realizing block 1/1 ... -#> OK +#> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 +#> / reading and realizing block 1/1 ... +#> ok #> \ Writing it ... #> OK #> Finished writing assay 2/5 to HDF5 file: -#> /tmp/RtmpswreTL/test_mae/miniACC_experiments.h5 +#> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> Start writing assay 3/5 to HDF5 file: -#> /tmp/RtmpswreTL/test_mae/miniACC_experiments.h5 -#> / Reading and realizing block 1/1 ... -#> OK +#> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 +#> / reading and realizing block 1/1 ... +#> ok #> \ Writing it ... #> OK #> Finished writing assay 3/5 to HDF5 file: -#> /tmp/RtmpswreTL/test_mae/miniACC_experiments.h5 +#> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> Start writing assay 4/5 to HDF5 file: -#> /tmp/RtmpswreTL/test_mae/miniACC_experiments.h5 -#> / Reading and realizing block 1/1 ... -#> OK +#> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 +#> / reading and realizing block 1/1 ... +#> ok #> \ Writing it ... #> OK #> Finished writing assay 4/5 to HDF5 file: -#> /tmp/RtmpswreTL/test_mae/miniACC_experiments.h5 +#> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> Start writing assay 5/5 to HDF5 file: -#> /tmp/RtmpswreTL/test_mae/miniACC_experiments.h5 -#> / Reading and realizing block 1/1 ... -#> OK +#> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 +#> / reading and realizing block 1/1 ... +#> ok #> \ Writing it ... #> OK #> Finished writing assay 5/5 to HDF5 file: -#> /tmp/RtmpswreTL/test_mae/miniACC_experiments.h5 +#> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> Serialize MultiAssayExperiment object to RDS file: -#> /tmp/RtmpswreTL/test_mae/miniACC_mae.rds +#> /tmp/RtmpRerB1M/test_mae/miniACC_mae.rds ## inspect the files in the dir list.files(testDir) @@ -257,27 +240,23 @@

    Examples

    -
    - -
    +
    -
    +
    + - - diff --git a/reference/MatchedAssayExperiment-class.html b/reference/MatchedAssayExperiment-class.html index f5929ca9..5afcd4f3 100644 --- a/reference/MatchedAssayExperiment-class.html +++ b/reference/MatchedAssayExperiment-class.html @@ -1,115 +1,84 @@ -MatchedAssayExperiment - A matched-samples MultiAssayExperiment class — MatchedAssayExperiment-class • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    This class supports the use of matched samples where an equal number of observations per biological unit are present in all assays.

    -
    +
    +

    Usage

    MatchedAssayExperiment(...)
    -
    -

    Arguments

    -
    ...
    +
    +

    Arguments

    + + +
    ...

    Either a single MultiAssayExperiment or the components to create a valid MultiAssayExperiment

    -
    -

    Value

    - - -

    A MatchedAssayExperiment object

    +
    +

    Value

    +

    A MatchedAssayExperiment object

    -
    -

    Functions

    - +
    +

    Functions

    +
    -
    -

    See also

    - +
    +

    See also

    +
    -
    -

    Examples

    +
    +

    Examples

    data("miniACC")
     acc <- as(miniACC, "MatchedAssayExperiment")
     acc
    @@ -132,27 +101,23 @@ 

    Examples

    -
    - -
    +
    -
    +
    + - - diff --git a/reference/MatchedAssayExperiment.html b/reference/MatchedAssayExperiment.html new file mode 100644 index 00000000..4ec9ef95 --- /dev/null +++ b/reference/MatchedAssayExperiment.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/MultiAssayExperiment-class.html b/reference/MultiAssayExperiment-class.html index e7273c85..b5ad3147 100644 --- a/reference/MultiAssayExperiment-class.html +++ b/reference/MultiAssayExperiment-class.html @@ -1,96 +1,70 @@ -MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class • MultiAssayExperimentMultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    The MultiAssayExperiment class can be used to manage results of diverse assays on a collection of specimen. Currently, the class can handle assays that are organized instances of SummarizedExperiment, -ExpressionSet, matrix, -RaggedExperiment +ExpressionSet, matrix, RaggedExperiment (inherits from GRangesList), and RangedVcfStack. Create new MultiAssayExperiment instances with the homonymous constructor, minimally with the argument ExperimentList, @@ -98,26 +72,27 @@

    MultiAssayExperiment - An integrative multi-assay class for experiment data< sampleMap.

    -
    -
    # S4 method for MultiAssayExperiment
    +    
    +

    Usage

    +
    # S4 method for class 'MultiAssayExperiment'
     show(object)
     
    -# S4 method for MultiAssayExperiment
    +# S4 method for class 'MultiAssayExperiment'
     length(x)
     
    -# S4 method for MultiAssayExperiment
    +# S4 method for class 'MultiAssayExperiment'
     names(x)
     
    -# S4 method for MultiAssayExperiment
    +# S4 method for class 'MultiAssayExperiment'
     updateObject(object, ..., verbose = FALSE)
     
    -# S4 method for MultiAssayExperiment
    +# S4 method for class 'MultiAssayExperiment'
     dimnames(x)
     
    -# S4 method for MultiAssayExperiment
    +# S4 method for class 'MultiAssayExperiment'
     c(x, ..., sampleMap = NULL, mapFrom = NULL)
     
    -# S4 method for MultiAssayExperiment
    +# S4 method for class 'MultiAssayExperiment'
     exportClass(
       object,
       dir = tempdir(),
    @@ -128,97 +103,97 @@ 

    MultiAssayExperiment - An integrative multi-assay class for experiment data< ... ) -# S4 method for MultiAssayExperiment +# S4 method for class 'MultiAssayExperiment' assays(x, withDimnames = TRUE, ...) -# S4 method for MultiAssayExperiment,missing +# S4 method for class 'MultiAssayExperiment,missing' assay(x, i, withDimnames = TRUE, ...) -# S4 method for MultiAssayExperiment,numeric +# S4 method for class 'MultiAssayExperiment,numeric' assay(x, i, withDimnames = TRUE, ...) -# S4 method for MultiAssayExperiment,character +# S4 method for class 'MultiAssayExperiment,character' assay(x, i, withDimnames = TRUE, ...)

    -
    -

    Arguments

    -
    object, x
    +
    +

    Arguments

    + + +
    object, x

    A MultiAssayExperiment object

    -
    ...
    +
    ...

    Additional arguments for supporting functions. See details.

    -
    verbose
    -

    logical(1) Whether to print additional information (default +

    verbose
    +

    logical(1) Whether to print additional information (default TRUE)

    -
    sampleMap
    +
    sampleMap

    c method: a sampleMap list or DataFrame to guide merge

    -
    mapFrom
    +
    mapFrom

    Either a logical, character, or integer vector indicating the experiment(s) that have an identical colname order as the experiment input(s). If using a character input, the name must match exactly.

    -
    dir
    -

    character(1) A directory for saving exported data (default: -`tempdir()`)

    +
    dir
    +

    character(1) A directory for saving exported data (default: +tempdir())

    -
    fmt
    -

    character(1) or function() Either a format character atomic as -supported by `write.table` either ('csv', or 'tsv') or a function whose +

    fmt
    +

    character(1) or function() Either a format character atomic as +supported by write.table either ('csv', or 'tsv') or a function whose first two arguments are 'object to save' and 'file location'

    -
    ext
    -

    character(1) A file extension supported by the format argument

    +
    ext
    +

    character(1) A file extension supported by the format argument

    -
    match
    -

    logical(1) Whether to coerce the current object to a +

    match
    +

    logical(1) Whether to coerce the current object to a 'MatchedAssayExperiment' object (default: FALSE)

    -
    withDimnames
    +
    withDimnames

    logical (default TRUE) whether to return dimension names included in the object

    -
    i
    +
    i

    An integer or character scalar indicating the assay to return

    -
    -

    Value

    - - -

    A MultiAssayExperiment object

    +
    +

    Value

    +

    A MultiAssayExperiment object

    -
    -

    Details

    +
    +

    Details

    The dots (...) argument allows the user to specify additional arguments in several instances.

    • subsetting [: additional arguments sent to -findOverlaps.

    • +findOverlaps.

    • mergeReplicates: used to specify arguments for the simplify functional argument

    • assay: may contain withDimnames, which is forwarded to assays

    • combining c: compatible MultiAssayExperiment classes -passed on to the ExperimentList constructor, +passed on to the ExperimentList constructor, can be a list, List, or a series of named arguments. See the examples below.

    -
    -

    Methods (by generic)

    - +
    +

    Methods (by generic)

    +
    • show(MultiAssayExperiment): Show method for a MultiAssayExperiment

    • length(MultiAssayExperiment): Get the length of ExperimentList

    • @@ -234,12 +209,12 @@

      Methods (by generic)

    • assays(MultiAssayExperiment): Obtain a SimpleList of assay data for all available experiments in the object

    • assay(x = MultiAssayExperiment, i = missing): Convenience function for extracting the -assay of the first element (default) in the ExperimentList. A -numeric or character index can also be provided

    • +assay of the first element (default) in the ExperimentList. A numeric +or character index can also be provided

    -
    -

    Slots

    - +
    +

    Slots

    +
    ExperimentList

    A ExperimentList class object for @@ -266,25 +241,25 @@

    Slots

    -
    -

    colData

    - +
    +

    colData

    +

    The colData slot is a collection of primary specimen data valid across all experiments. This slot is strictly of class -DataFrame but arguments for the constructor function +DataFrame but arguments for the constructor function allow arguments to be of class data.frame and subsequently coerced.

    -
    -

    ExperimentList

    - +
    +

    ExperimentList

    +

    The ExperimentList slot is designed to contain results from -each experiment/assay. It contains a SimpleList.

    +each experiment/assay. It contains a SimpleList.

    -
    -

    sampleMap

    - +
    +

    sampleMap

    +

    The sampleMap contains a DataFrame of translatable identifiers of samples and participants or biological units. The standard @@ -301,27 +276,27 @@

    sampleMap

    "assay" factor in the sampleMap do not match the names in the ExperimentList.

    -
    -

    coercion

    - +
    +

    coercion

    +

    Convert a list or S4 List to a MultiAssayExperiment object using the -as function.

    -

    In the following example, x is either a list or List:

    +methods::as function.

    +

    In the following example, x is either a list or List:

    as(x, "MultiAssayExperiment")

    Convert a MultiAssayExperiment to MAF class object using the -as function.

    -

    In the following example, x is a MultiAssayExperiment:

    +methods::as function.

    +

    In the following example, x is a MultiAssayExperiment:

    MultiAssayExperimentToMAF(x)

    -
    -

    See also

    +
    -
    -

    Examples

    +
    +

    Examples

    example("MultiAssayExperiment")
     #> 
     #> MltAsE> ## Run the example ExperimentList
    @@ -676,27 +651,23 @@ 

    Examples

    -
    - -
    +
    -
    +
    + - - diff --git a/reference/MultiAssayExperiment-helpers.html b/reference/MultiAssayExperiment-helpers.html index ba2fedb0..ae5e81ff 100644 --- a/reference/MultiAssayExperiment-helpers.html +++ b/reference/MultiAssayExperiment-helpers.html @@ -1,10 +1,50 @@ -A group of helper functions for manipulating and cleaning a -MultiAssayExperiment — MultiAssayExperiment-helpers • MultiAssayExperimentA group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    A set of helper functions were created to help clean and manipulate a MultiAssayExperiment object. intersectRows also works -for ExperimentList objects.

    -
    • complete.cases: Returns a logical vector corresponding to 'colData' +for ExperimentList objects.

      • complete.cases: Returns a logical vector corresponding to 'colData' rows that have data across all experiments

      • isEmpty: Returns a logical TRUE value for zero length MultiAssayExperiment objects

      • @@ -146,10 +151,10 @@

        A group of helper functions for manipulating and cleaning a measurements across all experiments and is guided by the replicated return value

      • longFormat: A MultiAssayExperiment method that -returns a small and skinny DataFrame. The colDataCols +returns a small and skinny DataFrame. The colDataCols arguments allows the user to append colData columns to the data.

      • wideFormat: A function to reshape the data in a -MultiAssayExperiment to a "wide" format DataFrame. Each row in +MultiAssayExperiment to a "wide" format DataFrame. Each row in the DataFrame represents an observation (corresponding to an entry in the colData). If replicates are present, their data will be appended at the end of the corresponding row and will generate additional NA data. @@ -157,7 +162,7 @@

        A group of helper functions for manipulating and cleaning a mergeReplicates. Optional colDataCols can be added when the original object is a MultiAssayExperiment.

      • hasRowRanges: A function that identifies ExperimentList elements -that have a rowRanges method

      • +that have a rowRanges method

      • getWithColData: A convenience function for extracting an assay and associated colData

      • renamePrimary: A convenience function to rename the primary @@ -166,11 +171,12 @@

        A group of helper functions for manipulating and cleaning a of a particular assay

    -
    -
    # S4 method for MultiAssayExperiment
    +    
    +

    Usage

    +
    # S4 method for class 'MultiAssayExperiment'
     complete.cases(...)
     
    -# S4 method for MultiAssayExperiment
    +# S4 method for class 'MultiAssayExperiment'
     isEmpty(x)
     
     intersectRows(x)
    @@ -179,27 +185,27 @@ 

    A group of helper functions for manipulating and cleaning a replicated(x) -# S4 method for MultiAssayExperiment +# S4 method for class 'MultiAssayExperiment' replicated(x) anyReplicated(x) -# S4 method for MultiAssayExperiment +# S4 method for class 'MultiAssayExperiment' anyReplicated(x) showReplicated(x) -# S4 method for MultiAssayExperiment +# S4 method for class 'MultiAssayExperiment' showReplicated(x) replicates(x, ...) -# S4 method for MultiAssayExperiment +# S4 method for class 'MultiAssayExperiment' replicates(x, ...) mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...) -# S4 method for MultiAssayExperiment +# S4 method for class 'MultiAssayExperiment' mergeReplicates( x, replicates = replicated(x), @@ -207,7 +213,7 @@

    A group of helper functions for manipulating and cleaning a ... ) -# S4 method for ANY +# S4 method for class 'ANY' mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...) longFormat(object, colDataCols = NULL, i = 1L) @@ -222,10 +228,10 @@

    A group of helper functions for manipulating and cleaning a hasRowRanges(x) -# S4 method for MultiAssayExperiment +# S4 method for class 'MultiAssayExperiment' hasRowRanges(x) -# S4 method for ExperimentList +# S4 method for class 'ExperimentList' hasRowRanges(x) getWithColData(x, i, mode = c("append", "replace"), verbose = FALSE) @@ -236,103 +242,103 @@

    A group of helper functions for manipulating and cleaning a splitAssays(x, hitList) -# S4 method for MultiAssayExperiment +# S4 method for class 'MultiAssayExperiment' splitAssays(x, hitList) makeHitList(x, patternList)

    -
    -

    Arguments

    -
    ...
    +
    +

    Arguments

    + + +
    ...

    Additional arguments. See details for more information.

    -
    x
    +
    x

    A MultiAssayExperiment or ExperimentList

    -
    replicates
    -

    A list of LogicalLists +

    replicates
    +

    A list of LogicalLists indicating multiple / duplicate entries for each biological unit per assay, see replicated (default replicated(x)).

    -
    simplify
    +
    simplify

    A function for merging repeat measurements in experiments as indicated by the replicated method for MultiAssayExperiment

    -
    object
    +
    object

    Any supported class object

    -
    colDataCols
    +
    colDataCols

    A character, logical, or numeric index for colData columns to be included

    -
    i
    +
    i

    longFormat: The i-th assay in -SummarizedExperiment-like objects. A vector input is -supported in the case that the SummarizedExperiment object(s) has more +SummarizedExperiment-like objects. A vector input is +supported in the case that the SummarizedExperiment object(s) has more than one assay (default 1L), renameColname: Either a numeric or character index indicating the assay whose colnames are to be renamed

    -
    check.names
    +
    check.names

    (logical default TRUE) Column names of the output DataFrame will be checked for syntactic validity and made unique, if necessary

    -
    collapse
    +
    collapse

    (character default "_") A single string delimiter for output column names. In wideFormat, experiments and rownames (and when replicate samples are present, colnames) are seperated by this delimiter

    -
    mode
    -

    String indicating how MultiAssayExperiment +

    mode
    +

    String indicating how MultiAssayExperiment column-level metadata should be added to the -SummarizedExperiment colData.

    +SummarizedExperiment colData.

    -
    verbose
    -

    logical(1) Whether to `suppressMessages` on subsetting -operations in `getWithColData` (default FALSE)

    +
    verbose
    +

    logical(1) Whether to suppressMessages on subsetting +operations in getWithColData (default FALSE)

    -
    value
    +
    value

    renamePrimary: A character vector of the same length as the existing rownames(colData) to use for replacement, renameColname: A CharacterList or list with matching lengths to replace colnames(x)

    -
    hitList
    +
    hitList

    a named list or List of logical vectors that indicate groupings in the assays

    -
    patternList
    +
    patternList

    a named list or List of atomic character vectors that are the input to grepl for identifying groupings in the assays

    -
    -

    Value

    - - -

    See the itemized list in the description section for details.

    +
    +

    Value

    +

    See the itemized list in the description section for details.

    -
    -

    Details

    +
    +

    Details

    The replicated function finds replicate measurements in each -assay and returns a list of LogicalLists. -Each element in a single LogicalList corresponds to a +assay and returns a list of LogicalLists. +Each element in a single LogicalList corresponds to a biological or primary unit as in the sampleMap. Below is a small graphic for one particular biological unit in one assay, where the logical vector corresponds to the number of measurements/samples in the @@ -345,15 +351,15 @@

    Details

    replicate. Note. These methods are not available for the ExperimentList class due to a missing sampleMap structure (by design). -showReplicated returns a list of CharacterLists where +showReplicated returns a list of CharacterLists where each element corresponds to the the biological or primary units that are replicated in that assay element. The values in the inner list are the colnames in the assay that are technical replicates.

    The replicates function (noun) returns the colnames - from the sampleMap that were identified as replicates. It returns a - list of CharacterLists for each assay present in the - MultiAssayExperiment and an inner entry for each biological unit - that has replicate observations in that assay.

    +from the sampleMap that were identified as replicates. It returns a +list of CharacterLists for each assay present in the +MultiAssayExperiment and an inner entry for each biological unit +that has replicate observations in that assay.

    The mergeReplicates function is a house-keeping method for a MultiAssayExperiment where only complete.cases are returned. This by-assay operation averages replicate measurements @@ -367,87 +373,86 @@

    Details

    user to provide additional arguments to the simplify functional argument.

    The longFormat "ANY" class method, works with classes such as -ExpressionSet and SummarizedExperiment as well as matrix -to provide a consistent long and skinny DataFrame.

    +ExpressionSet and SummarizedExperiment as well as matrix +to provide a consistent long and skinny DataFrame.

    The hasRowRanges method identifies assays that support -a rowRanges method and -return a GRanges object.

    +a rowRanges method and +return a GRanges object.

    -
    -

    mergeReplicates

    - +
    +

    mergeReplicates

    +

    The mergeReplicates function makes use of the output from replicated which will point out the duplicate measurements by biological unit in the MultiAssayExperiment. This function will return a MultiAssayExperiment with merged replicates. Additional arguments can be provided to the simplify argument via the ellipsis -(...). For example, when replicates "TCGA-B" and "TCGA-A" are found in +(...). For example, when replicates "TCGA-B" and "TCGA-A" are found in the assay, the name of the first appearing replicate is taken (i.e., "B"). Note that a typical use case of merging replicates occurs when there are multiple measurements on the same sample (within the same assay) and can therefore be averaged.

    -
    -

    longFormat

    - +
    +

    longFormat

    +

    The 'longFormat' method takes data from the ExperimentList -in a MultiAssayExperiment and returns a uniform -DataFrame. The resulting DataFrame has columns indicating +in a MultiAssayExperiment and returns a uniform +DataFrame. The resulting DataFrame has columns indicating primary, rowname, colname and value. This method can optionally include columns of the MultiAssayExperiment colData named by colDataCols character vector argument. (MultiAssayExperiment method only). The i argument allows the user to specify the assay value for the -SummarizedExperiment assay function's i argument.

    +SummarizedExperiment assay function's i argument.

    -
    -

    wideFormat

    - +
    +

    wideFormat

    -

    The wideFormat function returns standardized wide DataFrame + +

    The wideFormat function returns standardized wide DataFrame where each row represents a biological unit as in the colData. Depending on the data and setup, biological units can be patients, tumors, specimens, etc. Metadata columns are generated based on the names produced in the wide format -DataFrame. These can be accessed via the -mcols function. +DataFrame. These can be accessed via the +mcols() function. See the wideFormat section for description of the colDataCols and i arguments.

    -
    -

    hasRowRanges

    - +
    +

    hasRowRanges

    +

    The hasRowRanges method identifies assays with associated ranged row data by directly testing the method on the object. The result from the -test must be a GRanges class object to satisfy the test.

    +test must be a GRanges class object to satisfy the test.

    -
    -

    getWithColData

    - +
    +

    getWithColData

    +

    The getWithColData function allows the user to conveniently extract a particular assay as indicated by the i index argument. It will also attempt to provide the -colData along with the -extracted object using the colData<- replacement +colData +along with the extracted object using the colData<- replacement method when possible. Typically, this method is available for -SummarizedExperiment and RaggedExperiment -classes.

    +SummarizedExperiment and RaggedExperiment classes.

    The setting of mode determines how the colData -is added. If mode="append", the MultiAssayExperiment -metadata is appended onto that of the SummarizedExperiment. +is added. If mode="append", the MultiAssayExperiment +metadata is appended onto that of the SummarizedExperiment. If any fields are duplicated by name, the values in the -SummarizedExperiment are retained, with a warning emitted if +SummarizedExperiment are retained, with a warning emitted if the values are different. For mode="replace", the -MultiAssayExperiment metadata replaces that of the -SummarizedExperiment, while for mode="none", +MultiAssayExperiment metadata replaces that of the +SummarizedExperiment, while for mode="none", no replacement or appending is performed.

    -
    -

    rename*

    - +
    +

    rename*

    +

    The renamePrimary function allows the user to conveniently change the actual names of the primary biological units as seen in @@ -456,9 +461,9 @@

    rename*

    a single numeric or character value. See colnames<- method for renaming multiple colnames in a MultiAssayExperiment.

    -
    -

    splitAssays

    - +
    +

    splitAssays

    +

    The splitAssays method separates columns in each of the assays based on the hitList input. The hitList can be generated using @@ -468,8 +473,8 @@

    splitAssays

    to avoid repetition of columns across assays. See the examples section.

    -
    -

    Examples

    +
    +

    Examples

    
     example(MultiAssayExperiment)
     #> 
    @@ -657,27 +662,23 @@ 

    Examples

    -
    - -
    +
    -
    +
    + - - diff --git a/reference/MultiAssayExperiment-methods.html b/reference/MultiAssayExperiment-methods.html index 30c68382..85950800 100644 --- a/reference/MultiAssayExperiment-methods.html +++ b/reference/MultiAssayExperiment-methods.html @@ -1,207 +1,176 @@ -Accessing and modifying information in MultiAssayExperiment — MultiAssayExperiment-methods • MultiAssayExperimentAccessing and modifying information in MultiAssayExperiment — MultiAssayExperiment-methods • MultiAssayExperiment - - -
    -
    - - - -
    -
    - - -
    -

    A set of accessor and setter generic functions to extract -either the sampleMap, the ExperimentList, -colData, or metadata slots of a -MultiAssayExperiment object

    -
    - -
    -
    # S4 method for MultiAssayExperiment
    -sampleMap(x)
    -
    -# S4 method for MultiAssayExperiment
    -experiments(x)
    -
    -# S4 method for MultiAssayExperiment
    -colData(x, ...)
    -
    -# S4 method for MultiAssayExperiment
    -drops(x)
    -
    -# S4 method for MultiAssayExperiment,DataFrame
    -sampleMap(object) <- value
    +MultiAssayExperiment object">
    +    Skip to contents
     
    -# S4 method for MultiAssayExperiment,ANY
    -sampleMap(object) <- value
     
    -drops(x, ...) <- value
    +    
    +
    +
    -# S4 method for MultiAssayExperiment,list -colnames(x) <- value +
    +

    A set of accessor and setter generic functions to extract +either the sampleMap, the ExperimentList, +colData, or metadata slots of a +MultiAssayExperiment object

    +
    -# S4 method for MultiAssayExperiment -$(x, name) +
    +

    Usage

    +
    # S4 method for class 'MultiAssayExperiment'
    +sampleMap(x)
    +
    +# S4 method for class 'MultiAssayExperiment'
    +experiments(x)
    +
    +# S4 method for class 'MultiAssayExperiment'
    +colData(x, ...)
    +
    +# S4 method for class 'MultiAssayExperiment'
    +drops(x)
    +
    +# S4 method for class 'MultiAssayExperiment,DataFrame'
    +sampleMap(object) <- value
    +
    +# S4 method for class 'MultiAssayExperiment,ANY'
    +sampleMap(object) <- value
    +
    +drops(x, ...) <- value
    +
    +# S4 method for class 'MultiAssayExperiment,ExperimentList'
    +experiments(object) <- value
    +
    +# S4 method for class 'MultiAssayExperiment,List'
    +experiments(object) <- value
    +
    +# S4 method for class 'MultiAssayExperiment,DataFrame'
    +colData(x) <- value
    +
    +# S4 method for class 'MultiAssayExperiment,ANY'
    +colData(x) <- value
    +
    +# S4 method for class 'MultiAssayExperiment'
    +drops(x, ...) <- value
    +
    +# S4 method for class 'MultiAssayExperiment'
    +x$name <- value
    +
    +# S4 method for class 'MultiAssayExperiment'
    +names(x) <- value
    +
    +# S4 method for class 'MultiAssayExperiment,List'
    +colnames(x) <- value
    +
    +# S4 method for class 'MultiAssayExperiment,list'
    +colnames(x) <- value
    +
    +# S4 method for class 'MultiAssayExperiment'
    +x$name
    +
    +# S4 method for class 'MultiAssayExperiment'
    +metadata(x, ...)
    +
    +# S4 method for class 'MultiAssayExperiment'
    +metadata(x, ...) <- value
    +
    -# S4 method for MultiAssayExperiment -metadata(x, ...) +
    +

    Arguments

    -# S4 method for MultiAssayExperiment -metadata(x, ...) <- value
    -
    -
    -

    Arguments

    -
    ...
    +
    ...

    Argument not in use

    -
    object, x
    +
    object, x

    A MultiAssayExperiment object

    -
    value
    +
    value

    See details.

    -
    name
    +
    name

    A column in colData

    -
    -

    Value

    - - -

    Accessors: Either a sampleMap, ExperimentList, or +

    +

    Value

    +

    Accessors: Either a sampleMap, ExperimentList, or DataFrame object

    - -

    Setters: A MultiAssayExperiment object

    -
    -

    Accessors

    - +
    +

    Accessors

    +

    Eponymous names for accessing MultiAssayExperiment slots with the -exception of the ExperimentList accessor named experiments.

    • colData: Access the colData slot

    • +exception of the ExperimentList accessor named experiments.

    -
    -

    Setters

    - +
    +

    Setters

    +

    Setter method values (i.e., 'function(x) <- value'):

    • experiments<-: An ExperimentList object - containing experiment data of supported classes

    • +containing experiment data of supported classes

    • sampleMap<-: A DataFrame object relating - samples to biological units and assays

    • +samples to biological units and assays

    • colData<-: A DataFrame object describing the - biological units

    • +biological units

    • metadata<-: A list object of metadata

    • -
    • `[[<-`: Equivalent to the experiments<- setter method for - convenience

    • -
    • `$<-`: A vector to replace the indicated column in colData

    • -
    • `drops<-`: Trace ExperimentList names that have been - removed

    • +
    • [[<-: Equivalent to the experiments<- setter method for +convenience

    • +
    • $<-: A vector to replace the indicated column in colData

    • +
    • drops<-: Trace ExperimentList names that have been +removed

    -
    -

    Examples

    +
    +

    Examples

    ## Load example MultiAssayExperiment
     example(MultiAssayExperiment)
     #> 
    @@ -347,27 +316,23 @@ 

    Examples

    mae$age <- mae$age + 1
    -
    - -
    +
    -
    +
    + - - diff --git a/reference/MultiAssayExperiment-package.html b/reference/MultiAssayExperiment-package.html index 73080de2..fafcb434 100644 --- a/reference/MultiAssayExperiment-package.html +++ b/reference/MultiAssayExperiment-package.html @@ -1,83 +1,53 @@ -MultiAssayExperiment: Build an integrative multi-assay container — MultiAssayExperiment-package • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    MultiAssayExperiment allows the manipulation of related multiassay datasets with partially overlapping samples, associated metadata at the level of an entire study, and at the level of the "biological unit". @@ -85,46 +55,46 @@

    MultiAssayExperiment: Build an integrative multi-assay container

    -
    -

    Details

    +
    +

    Details

    The package hierarchy of information:

    • study

    • experiments

    • samples

    -
    -

    See also

    + -
    -

    Author

    +
    +

    Author

    Maintainer: Marcel Ramos marcel.ramos@roswellpark.org (ORCID)

    -

    Authors:

    Other contributors:

    -
    - -
    +
    -
    +
    + - - diff --git a/reference/MultiAssayExperiment.html b/reference/MultiAssayExperiment.html index 4a495fb8..e81cf0c6 100644 --- a/reference/MultiAssayExperiment.html +++ b/reference/MultiAssayExperiment.html @@ -1,95 +1,64 @@ -Construct an integrative representation of multi-omic data with -MultiAssayExperiment — MultiAssayExperiment • MultiAssayExperimentConstruct an integrative representation of multi-omic data with MultiAssayExperiment — MultiAssayExperiment • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    -

    The constructor function for the MultiAssayExperiment-class combines +

    +

    The constructor function for the MultiAssayExperiment combines multiple data elements from the different hierarchies of data (study, experiments, and samples). It can create instances where neither a sampleMap or a colData set is provided. Please see the MultiAssayExperiment API documentation for more information.

    -
    +
    +

    Usage

    MultiAssayExperiment(
       experiments = ExperimentList(),
       colData = S4Vectors::DataFrame(),
    @@ -100,84 +69,84 @@ 

    Construct an integrative representation of multi-omic data with )

    -
    -

    Arguments

    -
    experiments
    -

    A list or ExperimentList of all +

    +

    Arguments

    + + +
    experiments
    +

    A list or ExperimentList of all combined experiments

    -
    colData
    -

    A DataFrame or data.frame of +

    colData
    +

    A DataFrame or data.frame of characteristics for all biological units

    -
    sampleMap
    +
    sampleMap

    A DataFrame or data.frame of assay names, sample identifiers, and colname samples

    -
    metadata
    +
    metadata

    An optional argument of "ANY" class (usually list) for content describing the experiments

    -
    drops
    +
    drops

    A list of unmatched information (included after subsetting)

    -
    -

    Value

    - - -

    A MultiAssayExperiment object that can store +

    +

    Value

    +

    A MultiAssayExperiment object that can store experiment and phenotype data

    -
    -

    colData

    - +
    +

    colData

    + -

    The `colData` input can be either `DataFrame` or `data.frame` with -subsequent coercion to DataFrame. The rownames in the `colData` must match +

    The colData input can be either DataFrame or data.frame with +subsequent coercion to DataFrame. The rownames in the colData must match the colnames in the experiments if no sampleMap is provided.

    -
    -

    experiments

    - +
    +

    experiments

    -

    The `experiments` input can be of class SimpleList or `list`. + +

    The experiments input can be of class SimpleList or list. This input becomes the ExperimentList. Each element of the -input `list` or `List` must be named, rectangular with two dimensions, and -have `dimnames`.

    +input list or List must be named, rectangular with two dimensions, and +have dimnames.

    -
    -

    sampleMap

    - +
    +

    sampleMap

    + -

    The sampleMap can either be input as `DataFrame` or -`data.frame` with eventual coercion to `DataFrame`. The `sampleMap` relates +

    The sampleMap can either be input as DataFrame or +data.frame with eventual coercion to DataFrame. The sampleMap relates biological units and biological measurements within each assay. Each row in -the `sampleMap` is a single such link. The standard column names of the -`sampleMap` are "assay", "primary", and "colname". Note that the "assay" +the sampleMap is a single such link. The standard column names of the +sampleMap are "assay", "primary", and "colname". Note that the "assay" column is a factor corresponding to the names of each experiment in the -`ExperimentList`. In the case where these names do not match between the -`sampleMap` and the experiments, the documented experiments in the -`sampleMap` take precedence and experiments are dropped by the harmonization -procedure. The constructor function will generate a `sampleMap` in the case +ExperimentList. In the case where these names do not match between the +sampleMap and the experiments, the documented experiments in the +sampleMap take precedence and experiments are dropped by the harmonization +procedure. The constructor function will generate a sampleMap in the case where it is not provided and this method may be a 'safer' alternative for -creating the `MultiAssayExperiment` (so long as the rownames are identical -in the `colData`, if provided). An empty `sampleMap` may produce empty -experiments if the levels of the "assay" factor in the `sampleMap` do not -match the names in the `ExperimentList`.

    +creating the MultiAssayExperiment (so long as the rownames are identical +in the colData, if provided). An empty sampleMap may produce empty +experiments if the levels of the "assay" factor in the sampleMap do not +match the names in the ExperimentList.

    -
    -

    See also

    - +
    +

    See also

    +
    -
    -

    Examples

    +
    +

    Examples

    ## Run the example ExperimentList
     example("ExperimentList")
     #> 
    @@ -270,27 +239,23 @@ 

    Examples

    sampleMap = sampMap)
    -
    - -
    +
    -
    +
    + - - diff --git a/reference/MultiAssayExperimentToMAF.html b/reference/MultiAssayExperimentToMAF.html index 206f15e8..d61c227a 100644 --- a/reference/MultiAssayExperimentToMAF.html +++ b/reference/MultiAssayExperimentToMAF.html @@ -1,132 +1,101 @@ -Convert MultiAssayExperiment to MAF class — MultiAssayExperimentToMAF • MultiAssayExperimentConvert MultiAssayExperiment to MAF class — MultiAssayExperimentToMAF • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    Take a MultiAssayExperiment object with specific mutation assays and convert these into a maftools representation. The names provided via synAssay and nonSynAssay must match exactly those assays in the MultiAssayExperiment.

    -
    +
    +

    Usage

    MultiAssayExperimentToMAF(x, synAssay = "maf_syn", nonSynAssay = "maf_nonSyn")
    -
    -

    Arguments

    -
    x
    +
    +

    Arguments

    + + +
    x

    A MultiAssayExperiment object

    -
    synAssay
    -

    character(1) The name of the ExperimentList element in the +

    synAssay
    +

    character(1) The name of the ExperimentList element in the MultiAssayExperiment that identifies synonymous variant classifications.

    -
    nonSynAssay
    -

    character(1) The name of the ExperimentList element in +

    nonSynAssay
    +

    character(1) The name of the ExperimentList element in the MultiAssayExperiment that identifies non-synonymous variant classifications.

    -
    - -
    +
    -
    +
    + - - diff --git a/reference/Rplot002.png b/reference/Rplot002.png index 71f94e73..a2568b94 100644 Binary files a/reference/Rplot002.png and b/reference/Rplot002.png differ diff --git a/reference/Rplot003.png b/reference/Rplot003.png index ba0391b5..8e0a9ce1 100644 Binary files a/reference/Rplot003.png and b/reference/Rplot003.png differ diff --git a/reference/[,MultiAssayExperiment,ANY,ANY,ANY-method.html b/reference/[,MultiAssayExperiment,ANY,ANY,ANY-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/[,MultiAssayExperiment,ANY,ANY,ANY-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/[,MultiAssayExperiment,ANY-method.html b/reference/[,MultiAssayExperiment,ANY-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/[,MultiAssayExperiment,ANY-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/[[,MultiAssayExperiment,ANY,ANY-method.html b/reference/[[,MultiAssayExperiment,ANY,ANY-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/[[,MultiAssayExperiment,ANY,ANY-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/anyReplicated,MultiAssayExperiment-method.html b/reference/anyReplicated,MultiAssayExperiment-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/anyReplicated,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/anyReplicated.html b/reference/anyReplicated.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/anyReplicated.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/assay,ANY,missing-method.html b/reference/assay,ANY,missing-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/assay,ANY,missing-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/assay,ExperimentList,character-method.html b/reference/assay,ExperimentList,character-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/assay,ExperimentList,character-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/assay,ExperimentList,missing-method.html b/reference/assay,ExperimentList,missing-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/assay,ExperimentList,missing-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/assay,ExperimentList,numeric-method.html b/reference/assay,ExperimentList,numeric-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/assay,ExperimentList,numeric-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/assay,MultiAssayExperiment,character-method.html b/reference/assay,MultiAssayExperiment,character-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/assay,MultiAssayExperiment,character-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/assay,MultiAssayExperiment,missing-method.html b/reference/assay,MultiAssayExperiment,missing-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/assay,MultiAssayExperiment,missing-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/assay,MultiAssayExperiment,numeric-method.html b/reference/assay,MultiAssayExperiment,numeric-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/assay,MultiAssayExperiment,numeric-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/assays,ExperimentList-method.html b/reference/assays,ExperimentList-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/assays,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/assays,MultiAssayExperiment-method.html b/reference/assays,MultiAssayExperiment-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/assays,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/c,MultiAssayExperiment-method.html b/reference/c,MultiAssayExperiment-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/c,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/coerce,List,ExperimentList-method.html b/reference/coerce,List,ExperimentList-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/coerce,List,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/coerce,List,MultiAssayExperiment-method.html b/reference/coerce,List,MultiAssayExperiment-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/coerce,List,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/coerce,MultiAssayExperiment,MatchedAssayExperiment-method.html b/reference/coerce,MultiAssayExperiment,MatchedAssayExperiment-method.html new file mode 100644 index 00000000..4ec9ef95 --- /dev/null +++ b/reference/coerce,MultiAssayExperiment,MatchedAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/coerce,list,ExperimentList-method.html b/reference/coerce,list,ExperimentList-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/coerce,list,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/coerce,list,MultiAssayExperiment-method.html b/reference/coerce,list,MultiAssayExperiment-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/coerce,list,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/coerce-ExperimentList.html b/reference/coerce-ExperimentList.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/coerce-ExperimentList.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/coerce-MultiAssayExperiment.html b/reference/coerce-MultiAssayExperiment.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/coerce-MultiAssayExperiment.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/colData,MultiAssayExperiment-method.html b/reference/colData,MultiAssayExperiment-method.html new file mode 100644 index 00000000..71716772 --- /dev/null +++ b/reference/colData,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/colnames,ExperimentList-method.html b/reference/colnames,ExperimentList-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/colnames,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/complete.cases,MultiAssayExperiment-method.html b/reference/complete.cases,MultiAssayExperiment-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/complete.cases,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/dimnames,ExperimentList-method.html b/reference/dimnames,ExperimentList-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/dimnames,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/dimnames,MultiAssayExperiment-method.html b/reference/dimnames,MultiAssayExperiment-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/dimnames,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/drops,MultiAssayExperiment-method.html b/reference/drops,MultiAssayExperiment-method.html new file mode 100644 index 00000000..71716772 --- /dev/null +++ b/reference/drops,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/drops.html b/reference/drops.html new file mode 100644 index 00000000..71716772 --- /dev/null +++ b/reference/drops.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/experiments,MultiAssayExperiment-method.html b/reference/experiments,MultiAssayExperiment-method.html new file mode 100644 index 00000000..71716772 --- /dev/null +++ b/reference/experiments,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/experiments.html b/reference/experiments.html new file mode 100644 index 00000000..71716772 --- /dev/null +++ b/reference/experiments.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/exportClass,MultiAssayExperiment-method.html b/reference/exportClass,MultiAssayExperiment-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/exportClass,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/exportClass.html b/reference/exportClass.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/exportClass.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/getWithColData.html b/reference/getWithColData.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/getWithColData.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/hasAssay.html b/reference/hasAssay.html index 7a3bbe15..bc0b6c12 100644 --- a/reference/hasAssay.html +++ b/reference/hasAssay.html @@ -1,136 +1,103 @@ -Checking assay method for any class — hasAssay • MultiAssayExperimentChecking assay method for any class — hasAssay • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    The hasAssay function is intended for developers who would like to include new classes into a MultiAssayExperiment instance. It checks the methods tables of the assay function for the specified class of the argument.

    -
    +
    +

    Usage

    hasAssay(object)
    -
    -

    Arguments

    -
    object
    +
    +

    Arguments

    + + +
    object

    A MultiAssayExperiment or named list object instance

    -
    -

    Value

    - - -

    A logical value indicating method availability

    +
    +

    Value

    +

    A logical value indicating method availability

    -
    -

    Examples

    +
    +

    Examples

    lst <- structure(list(), .Names=character())
     hasAssay(lst)
     #> [1] TRUE
     
     
    -
    - -
    +
    -
    +
    + - - diff --git a/reference/hasRowRanges,ExperimentList-method.html b/reference/hasRowRanges,ExperimentList-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/hasRowRanges,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/hasRowRanges,MultiAssayExperiment-method.html b/reference/hasRowRanges,MultiAssayExperiment-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/hasRowRanges,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/hasRowRanges.html b/reference/hasRowRanges.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/hasRowRanges.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/index.html b/reference/index.html index 271e7427..7e5ed23b 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,202 +1,247 @@ -Function reference • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -

    Classes

    -

    Exported classes

    -
    -

    show(<ExperimentList>) isEmpty(<ExperimentList>) dimnames(<ExperimentList>) colnames(<ExperimentList>) rownames(<ExperimentList>) mergeReplicates(<ExperimentList>) assay(<ANY>,<missing>) assays(<ExperimentList>) assay(<ExperimentList>,<missing>) assay(<ExperimentList>,<numeric>) assay(<ExperimentList>,<character>)

    -

    ExperimentList - A container for multi-experiment data

    -

    show(<MultiAssayExperiment>) length(<MultiAssayExperiment>) names(<MultiAssayExperiment>) updateObject(<MultiAssayExperiment>) dimnames(<MultiAssayExperiment>) c(<MultiAssayExperiment>) exportClass(<MultiAssayExperiment>) assays(<MultiAssayExperiment>) assay(<MultiAssayExperiment>,<missing>) assay(<MultiAssayExperiment>,<numeric>) assay(<MultiAssayExperiment>,<character>)

    -

    MultiAssayExperiment - An integrative multi-assay class for experiment data

    -

    MatchedAssayExperiment()

    -

    MatchedAssayExperiment - A matched-samples MultiAssayExperiment class

    -

    Constructors

    -

    Build objects with designated constructor functions

    -
    -

    MultiAssayExperiment()

    -

    Construct an integrative representation of multi-omic data with -MultiAssayExperiment

    -

    ExperimentList()

    -

    Represent multiple experiments as a List-derivative ExperimentList

    -

    Methods and Accessors

    -

    Discover content within MultiAssayExperiment

    -
    -

    show(<MultiAssayExperiment>) length(<MultiAssayExperiment>) names(<MultiAssayExperiment>) updateObject(<MultiAssayExperiment>) dimnames(<MultiAssayExperiment>) c(<MultiAssayExperiment>) exportClass(<MultiAssayExperiment>) assays(<MultiAssayExperiment>) assay(<MultiAssayExperiment>,<missing>) assay(<MultiAssayExperiment>,<numeric>) assay(<MultiAssayExperiment>,<character>)

    -

    MultiAssayExperiment - An integrative multi-assay class for experiment data

    -

    sampleMap(<MultiAssayExperiment>) experiments(<MultiAssayExperiment>) colData(<MultiAssayExperiment>) drops(<MultiAssayExperiment>) `sampleMap<-`(<MultiAssayExperiment>,<DataFrame>) `sampleMap<-`(<MultiAssayExperiment>,<ANY>) `drops<-`() `experiments<-`(<MultiAssayExperiment>,<ExperimentList>) `experiments<-`(<MultiAssayExperiment>,<List>) `colData<-`(<MultiAssayExperiment>,<DataFrame>) `colData<-`(<MultiAssayExperiment>,<ANY>) `$<-`(<MultiAssayExperiment>) `names<-`(<MultiAssayExperiment>) `colnames<-`(<MultiAssayExperiment>,<List>) `colnames<-`(<MultiAssayExperiment>,<list>) `$`(<MultiAssayExperiment>) metadata(<MultiAssayExperiment>) `metadata<-`(<MultiAssayExperiment>)

    -

    Accessing and modifying information in MultiAssayExperiment

    -

    Subsetting

    -

    Easy operations for selecting rows, columns, and/or biological units

    -
    -

    subsetByRow() subsetByColData() subsetByColumn() subsetByAssay() `[`(<MultiAssayExperiment>,<ANY>,<ANY>,<ANY>) `[[`(<MultiAssayExperiment>,<ANY>,<ANY>) `[[<-`(<MultiAssayExperiment>,<ANY>,<ANY>) `[<-`(<MultiAssayExperiment>,<ANY>,<ANY>,<ANY>)

    -

    Subsetting a MultiAssayExperiment object

    -

    Management and Reshaping

    -

    Work with and reshape data

    -
    -

    complete.cases(<MultiAssayExperiment>) isEmpty(<MultiAssayExperiment>) intersectRows() intersectColumns() replicated() anyReplicated() showReplicated() replicates() mergeReplicates() longFormat() wideFormat() hasRowRanges() getWithColData() renamePrimary() renameColname() splitAssays() makeHitList()

    -

    A group of helper functions for manipulating and cleaning a -MultiAssayExperiment

    -

    upsetSamples()

    -

    Create a generalized Venn Diagram analog for sample membership in multiple -assays, using the upset algorithm in UpSetR

    -

    listToMap() mapToList()

    -

    Convert map from data.frame or DataFrame to list and vice versa

    -

    prepMultiAssay()

    -

    Prepare a MultiAssayExperiment instance

    -

    External Formats

    -

    Compatibility with other Bioconductor packages

    -
    -

    saveHDF5MultiAssayExperiment() loadHDF5MultiAssayExperiment()

    -

    Save a MultiAssayExperiment class object to HDF5 and Rds files

    -

    MultiAssayExperimentToMAF()

    -

    Convert MultiAssayExperiment to MAF class

    -

    Misc. Package Docs

    -

    Other package information and data

    -
    -

    -

    MultiAssayExperiment: Build an integrative multi-assay container

    -

    hasAssay()

    -

    Checking assay method for any class

    -

    reexports DataFrame

    -

    Objects exported from other packages

    -

    miniACC

    -

    Adrenocortical Carcinoma (ACC) MultiAssayExperiment

    - - -
    +
    +

    Classes

    + +

    Exported classes

    + + +
    +

    Constructors

    + +

    Build objects with designated constructor functions

    + + +
    + + + + +
    + + MultiAssayExperiment() + +
    +
    Construct an integrative representation of multi-omic data with MultiAssayExperiment
    +
    + + ExperimentList() + +
    +
    Represent multiple experiments as a List-derivative ExperimentList
    +
    +

    Methods and Accessors

    + +

    Discover content within MultiAssayExperiment

    + + +
    +

    Subsetting

    + +

    Easy operations for selecting rows, columns, and/or biological units

    + + +
    -
    + + +
    -
    -

    Site built with pkgdown 2.0.7.

    + -
    +
    + - - diff --git a/reference/intersectColumns.html b/reference/intersectColumns.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/intersectColumns.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/intersectRows.html b/reference/intersectRows.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/intersectRows.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/isEmpty,ExperimentList-method.html b/reference/isEmpty,ExperimentList-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/isEmpty,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/isEmpty,MultiAssayExperiment-method.html b/reference/isEmpty,MultiAssayExperiment-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/isEmpty,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/length,MultiAssayExperiment-method.html b/reference/length,MultiAssayExperiment-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/length,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/loadHDF5MultiAssayExperiment.html b/reference/loadHDF5MultiAssayExperiment.html new file mode 100644 index 00000000..347ba713 --- /dev/null +++ b/reference/loadHDF5MultiAssayExperiment.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/longFormat.html b/reference/longFormat.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/longFormat.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/makeHitList.html b/reference/makeHitList.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/makeHitList.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/makeMatchList.html b/reference/makeMatchList.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/makeMatchList.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/mapToList.html b/reference/mapToList.html index 03d71438..1a650f00 100644 --- a/reference/mapToList.html +++ b/reference/mapToList.html @@ -1,132 +1,100 @@ -Convert map from data.frame or DataFrame to list and vice versa — listToMap • MultiAssayExperimentConvert map from data.frame or DataFrame to list and vice versa — listToMap • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    The mapToList function provides a convenient way of reordering a data.frame to a list. The listToMap function does the opposite by taking a list and converting it to DataFrame.

    -
    +
    +

    Usage

    listToMap(listmap, fill = TRUE)
     
     mapToList(dfmap, assayCol = "assay")
    -
    -

    Arguments

    -
    listmap
    +
    +

    Arguments

    + + +
    listmap

    A named list object containing DataFrames with "primary" and "colname" columns

    -
    fill
    -

    logical(1) Whether to fill the map with an empty DataFrame +

    fill
    +

    logical(1) Whether to fill the map with an empty DataFrame when empty elements are present in the input list

    -
    dfmap
    +
    dfmap

    A data.frame or DataFrame object with identifiers in the first column

    -
    assayCol
    +
    assayCol

    A character vector of length one indicating the assay names column

    -
    -

    Value

    - - -

    A DataFrame class object of names

    - - +
    +

    Value

    +

    A DataFrame class object of names

    A list object of DataFrames for each assay

    -
    -

    Functions

    - +
    +

    Functions

    +
    • listToMap(): The inverse of the listToMap operation

    -
    -

    Examples

    +
    +

    Examples

    example("MultiAssayExperiment")
     #> 
     #> MltAsE> ## Run the example ExperimentList
    @@ -228,27 +196,23 @@ 

    Examples

    maplist <- mapToList(sampMap)
    -
    - -
    +
    -
    +
    + - - diff --git a/reference/mergeReplicates,ANY-method.html b/reference/mergeReplicates,ANY-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/mergeReplicates,ANY-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/mergeReplicates,ExperimentList-method.html b/reference/mergeReplicates,ExperimentList-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/mergeReplicates,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/mergeReplicates,MultiAssayExperiment-method.html b/reference/mergeReplicates,MultiAssayExperiment-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/mergeReplicates,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/mergeReplicates.html b/reference/mergeReplicates.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/mergeReplicates.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/metadata,MultiAssayExperiment-method.html b/reference/metadata,MultiAssayExperiment-method.html new file mode 100644 index 00000000..71716772 --- /dev/null +++ b/reference/metadata,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/miniACC.html b/reference/miniACC.html index 30665c05..2c77f2b3 100644 --- a/reference/miniACC.html +++ b/reference/miniACC.html @@ -1,86 +1,59 @@ -Adrenocortical Carcinoma (ACC) MultiAssayExperiment — miniACC • MultiAssayExperimentAdrenocortical Carcinoma (ACC) MultiAssayExperiment — miniACC • MultiAssayExperiment - +additional details are provided by metadata(miniACC)."> + Skip to contents -
    -
    +
    +
    +
    -
    - -
    +

    A MultiAssayExperiment object providing a reduced version of the TCGA ACC dataset for all 92 patients. RNA-seq, copy number, and somatic mutations are included only for genes whose proteins are included in the @@ -90,55 +63,56 @@

    Adrenocortical Carcinoma (ACC) MultiAssayExperiment

    additional details are provided by metadata(miniACC).

    -
    +
    +

    Usage

    data("miniACC")
    -
    -

    Format

    +
    +

    Format

    A MultiAssayExperiment with 5 experiments, providing:

    RNASeq2GeneNorm

    RNA-seq count data: an ExpressionSet - with 198 rows and 79 columns

    +with 198 rows and 79 columns

    -
    gistict
    +
    gistict

    Reccurent copy number lesions identified by GISTIC2: - a SummarizedExperiment with 198 rows and 90 columns

    +a SummarizedExperiment with 198 rows and 90 columns

    -
    RPPAArray
    +
    RPPAArray

    Reverse Phase Protein Array: an ExpressionSet - with 33 rows and 46 columns. Rows are indexed by genes, - but protein annotations are available from - featureData(miniACC[["RPPAArray"]]). The source of these - annotations is noted in abstract(miniACC[["RPPAArray"]])

    +with 33 rows and 46 columns. Rows are indexed by genes, +but protein annotations are available from +featureData(miniACC[["RPPAArray"]]). The source of these +annotations is noted in abstract(miniACC[["RPPAArray"]])

    -
    Mutations
    +
    Mutations

    Somatic mutations: a matrix with 223 rows and - 90 columns. 1 for any kind of non-silent mutation, zero for silent - (synonymous) or no mutation.

    +90 columns. 1 for any kind of non-silent mutation, zero for silent +(synonymous) or no mutation.

    -
    miRNASeqGene
    +
    miRNASeqGene

    microRNA sequencing: an ExpressionSet with - 471 rows and 80 columns. Rows not having at least 5 counts in at least - 5 samples were removed.

    +471 rows and 80 columns. Rows not having at least 5 counts in at least +5 samples were removed.

    -
    -

    Source

    +
    +

    Source

    https://github.com/waldronlab/multiassayexperiment-tcga

    -
    -

    References

    -

    Zheng S *et al.*: Comprehensive Pan-Genomic Characterization of +

    +

    References

    +

    Zheng S et al.: Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell 2016, 29:723-736.

    -
    -

    Author

    +
    +

    Author

    Levi Waldron lwaldron.research@gmail.com

    -
    -

    Examples

    +
    +

    Examples

    
     data("miniACC")
     metadata(miniACC)
    @@ -199,32 +173,32 @@ 

    Examples

    #> harmonizing input: #> removing 216 sampleMap rows not in names(experiments) #> DataFrame with 169 rows and 7 columns -#> assay primary rowname colname value -#> <character> <character> <character> <character> <numeric> -#> 1 RNASeq2GeneNorm TCGA-OR-A5J1 MAPK3 TCGA-OR-A5J1-01A-11R.. 946.681 -#> 2 RNASeq2GeneNorm TCGA-OR-A5J2 MAPK3 TCGA-OR-A5J2-01A-11R.. 1699.382 -#> 3 RNASeq2GeneNorm TCGA-OR-A5J3 MAPK3 TCGA-OR-A5J3-01A-11R.. 2347.243 -#> 4 RNASeq2GeneNorm TCGA-OR-A5J5 MAPK3 TCGA-OR-A5J5-01A-11R.. 1299.156 -#> 5 RNASeq2GeneNorm TCGA-OR-A5J6 MAPK3 TCGA-OR-A5J6-01A-31R.. 2543.424 -#> ... ... ... ... ... ... -#> 165 gistict TCGA-PA-A5YG MAPK3 TCGA-PA-A5YG-01A-11D.. 1 -#> 166 gistict TCGA-PK-A5H9 MAPK3 TCGA-PK-A5H9-01A-11D.. 0 -#> 167 gistict TCGA-PK-A5HA MAPK3 TCGA-PK-A5HA-01A-11D.. 0 -#> 168 gistict TCGA-PK-A5HB MAPK3 TCGA-PK-A5HB-01A-11D.. 0 -#> 169 gistict TCGA-PK-A5HC MAPK3 TCGA-PK-A5HC-01A-11D.. 1 -#> vital_status days_to_death -#> <integer> <integer> -#> 1 1 1355 -#> 2 1 1677 -#> 3 0 NA -#> 4 1 365 -#> 5 0 NA -#> ... ... ... -#> 165 0 NA -#> 166 0 NA -#> 167 0 NA -#> 168 0 NA -#> 169 0 NA +#> assay primary rowname colname +#> <character> <character> <character> <factor> +#> 1 RNASeq2GeneNorm TCGA-OR-A5J1 MAPK3 TCGA-OR-A5J1-01A-11R-A29S-07 +#> 2 RNASeq2GeneNorm TCGA-OR-A5J2 MAPK3 TCGA-OR-A5J2-01A-11R-A29S-07 +#> 3 RNASeq2GeneNorm TCGA-OR-A5J3 MAPK3 TCGA-OR-A5J3-01A-11R-A29S-07 +#> 4 RNASeq2GeneNorm TCGA-OR-A5J5 MAPK3 TCGA-OR-A5J5-01A-11R-A29S-07 +#> 5 RNASeq2GeneNorm TCGA-OR-A5J6 MAPK3 TCGA-OR-A5J6-01A-31R-A29S-07 +#> ... ... ... ... ... +#> 165 gistict TCGA-PA-A5YG MAPK3 TCGA-PA-A5YG-01A-11D-A29H-01 +#> 166 gistict TCGA-PK-A5H9 MAPK3 TCGA-PK-A5H9-01A-11D-A29H-01 +#> 167 gistict TCGA-PK-A5HA MAPK3 TCGA-PK-A5HA-01A-11D-A29H-01 +#> 168 gistict TCGA-PK-A5HB MAPK3 TCGA-PK-A5HB-01A-11D-A29H-01 +#> 169 gistict TCGA-PK-A5HC MAPK3 TCGA-PK-A5HC-01A-11D-A309-01 +#> value vital_status days_to_death +#> <numeric> <integer> <integer> +#> 1 946.681 1 1355 +#> 2 1699.382 1 1677 +#> 3 2347.243 0 NA +#> 4 1299.156 1 365 +#> 5 2543.424 0 NA +#> ... ... ... ... +#> 165 1 0 NA +#> 166 0 0 NA +#> 167 0 0 NA +#> 168 0 0 NA +#> 169 1 0 NA wideFormat( miniACC["MAPK3", , ], @@ -249,27 +223,23 @@

    Examples

    -
    - -
    +
    -
    +
    + - - diff --git a/reference/names,MultiAssayExperiment-method.html b/reference/names,MultiAssayExperiment-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/names,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/prepMultiAssay.html b/reference/prepMultiAssay.html index 0eb380ca..ecf0da1f 100644 --- a/reference/prepMultiAssay.html +++ b/reference/prepMultiAssay.html @@ -1,126 +1,97 @@ -Prepare a MultiAssayExperiment instance — prepMultiAssay • MultiAssayExperimentPrepare a MultiAssayExperiment instance — prepMultiAssay • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    The purpose of this helper function is to faciltate the creation of a MultiAssayExperiment object by detecting any inconsistencies with all types of names in either the ExperimentList, the colData, or sampleMap.

    -
    +
    +

    Usage

    prepMultiAssay(ExperimentList, colData, sampleMap, ...)
    -
    -

    Arguments

    -
    ExperimentList
    +
    +

    Arguments

    + + +
    ExperimentList

    A list of all combined experiments

    -
    colData
    -

    A DataFrame of the phenotype +

    colData
    +

    A DataFrame of the phenotype data for all participants

    -
    sampleMap
    -

    A DataFrame of sample identifiers, assay +

    sampleMap
    +

    A DataFrame of sample identifiers, assay samples, and assay names

    -
    ...
    +
    ...

    Optional arguments for the MultiAssayExperiment constructor function such as metadata and drops.

    -
    -

    Value

    - - -

    A list containing all the essential components of a +

    +

    Value

    +

    A list containing all the essential components of a MultiAssayExperiment as well as a "drops" metadata element that indicates non-matched names. The names of the resulting list correspond to the arguments of the MultiAssayExperiment constructor function.

    -
    -

    Checks

    - +
    +

    Checks

    +

    The prepMultiAssay function checks that all columns in the sampleMap are character.

    @@ -141,8 +112,8 @@

    Checks

    necessary.

    -
    -

    Examples

    +
    +

    Examples

    ## Run example
     example("MultiAssayExperiment")
     #> 
    @@ -281,27 +252,23 @@ 

    Examples

    -
    - -
    +
    -
    +
    + - - diff --git a/reference/reexports.html b/reference/reexports.html index fde9855a..a98ecc53 100644 --- a/reference/reexports.html +++ b/reference/reexports.html @@ -1,120 +1,87 @@ -Objects exported from other packages — reexports • MultiAssayExperimentObjects exported from other packages — reexports • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    These objects are imported from other packages. Click on the function name to see their documentation.

    -
    -
    -

    Examples

    +
    +

    Examples

    DataFrame()
     #> DataFrame with 0 rows and 0 columns
     
     
    -
    - -
    +
    -
    +
    + - - diff --git a/reference/renameColname.html b/reference/renameColname.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/renameColname.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/renamePrimary.html b/reference/renamePrimary.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/renamePrimary.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/replicated,MultiAssayExperiment-method.html b/reference/replicated,MultiAssayExperiment-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/replicated,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/replicated.html b/reference/replicated.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/replicated.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/replicates,MultiAssayExperiment-method.html b/reference/replicates,MultiAssayExperiment-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/replicates,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/replicates.html b/reference/replicates.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/replicates.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/rownames,ExperimentList-method.html b/reference/rownames,ExperimentList-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/rownames,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/sampleMap,MultiAssayExperiment-method.html b/reference/sampleMap,MultiAssayExperiment-method.html new file mode 100644 index 00000000..71716772 --- /dev/null +++ b/reference/sampleMap,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/sampleMap.html b/reference/sampleMap.html new file mode 100644 index 00000000..71716772 --- /dev/null +++ b/reference/sampleMap.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/show,ExperimentList-method.html b/reference/show,ExperimentList-method.html new file mode 100644 index 00000000..0088df12 --- /dev/null +++ b/reference/show,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/show,MultiAssayExperiment-method.html b/reference/show,MultiAssayExperiment-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/show,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/showReplicated,MultiAssayExperiment-method.html b/reference/showReplicated,MultiAssayExperiment-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/showReplicated,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/showReplicated.html b/reference/showReplicated.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/showReplicated.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/splitAssays,MultiAssayExperiment-method.html b/reference/splitAssays,MultiAssayExperiment-method.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/splitAssays,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/splitAssays.html b/reference/splitAssays.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/splitAssays.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subset.html b/reference/subset.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subset.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetBy.html b/reference/subsetBy.html index d4a43f3d..ae870bab 100644 --- a/reference/subsetBy.html +++ b/reference/subsetBy.html @@ -1,195 +1,164 @@ -Subsetting a MultiAssayExperiment object — subsetBy • MultiAssayExperiment - - -
    -
    - - - -
    -
    - - -
    -

    A set of functions for extracting and dividing a -MultiAssayExperiment

    -
    - -
    -
    subsetByRow(x, y, ...)
    -
    -subsetByColData(x, y)
    -
    -subsetByColumn(x, y)
    -
    -subsetByAssay(x, y)
    -
    -# S4 method for ExperimentList,ANY
    -subsetByRow(x, y, ...)
    -
    -# S4 method for ExperimentList,list
    -subsetByRow(x, y)
    +Subsetting a MultiAssayExperiment object — subsetBy • MultiAssayExperiment
    +    Skip to contents
     
    -# S4 method for ExperimentList,List
    -subsetByRow(x, y)
     
    -# S4 method for ExperimentList,logical
    -subsetByRow(x, y)
    +    
    +
    +
    -# S4 method for MultiAssayExperiment,ANY,ANY,ANY -[(x, i, j, k, ..., drop = FALSE) +
    +

    A set of functions for extracting and dividing a +MultiAssayExperiment

    +
    -# S4 method for MultiAssayExperiment,ANY,ANY -[[(x, i, j, ...) +
    +

    Usage

    +
    subsetByRow(x, y, ...)
    +
    +subsetByColData(x, y)
    +
    +subsetByColumn(x, y)
    +
    +subsetByAssay(x, y)
    +
    +# S4 method for class 'ExperimentList,ANY'
    +subsetByRow(x, y, ...)
    +
    +# S4 method for class 'ExperimentList,list'
    +subsetByRow(x, y)
    +
    +# S4 method for class 'ExperimentList,List'
    +subsetByRow(x, y)
    +
    +# S4 method for class 'ExperimentList,logical'
    +subsetByRow(x, y)
    +
    +# S4 method for class 'ExperimentList,list'
    +subsetByColumn(x, y)
    +
    +# S4 method for class 'ExperimentList,List'
    +subsetByColumn(x, y)
    +
    +# S4 method for class 'ExperimentList,logical'
    +subsetByColumn(x, y)
    +
    +# S4 method for class 'ExperimentList'
    +subsetByAssay(x, y)
    +
    +# S4 method for class 'MultiAssayExperiment,ANY'
    +subsetByColData(x, y)
    +
    +# S4 method for class 'MultiAssayExperiment,character'
    +subsetByColData(x, y)
    +
    +# S4 method for class 'MultiAssayExperiment,ANY'
    +subsetByRow(x, y, ...)
    +
    +# S4 method for class 'MultiAssayExperiment,ANY'
    +subsetByColumn(x, y)
    +
    +# S4 method for class 'MultiAssayExperiment'
    +subsetByAssay(x, y)
    +
    +# S4 method for class 'MultiAssayExperiment,ANY,ANY,ANY'
    +x[i, j, k, ..., drop = FALSE]
    +
    +# S4 method for class 'MultiAssayExperiment,ANY,ANY'
    +x[[i, j, ...]]
    +
    +# S4 method for class 'MultiAssayExperiment,ANY,ANY'
    +x[[i, j, ...]] <- value
    +
    +# S4 method for class 'MultiAssayExperiment,ANY,ANY,ANY'
    +x[i, j, ...] <- value
    +
    -# S4 method for MultiAssayExperiment,ANY,ANY -[[(x, i, j, ...) <- value +
    +

    Arguments

    -# S4 method for MultiAssayExperiment,ANY,ANY,ANY -[(x, i, j, ...) <- value
    -
    -
    -

    Arguments

    -
    x
    +
    x

    A MultiAssayExperiment or ExperimentList

    -
    y
    +
    y

    Any argument used for subsetting, can be a character, logical, integer, list or List vector

    -
    ...
    +
    ...

    Additional arguments passed on to lower level functions.

    -
    i
    +
    i

    Either a character, integer, logical or GRanges object for subsetting by rows

    -
    j
    +
    j

    Either a character, logical, or numeric vector for subsetting by colData rows. See details for more information.

    -
    k
    +
    k

    Either a character, logical, or numeric vector for subsetting by assays

    -
    drop
    +
    drop

    logical (default FALSE) whether to drop all empty assay elements in the ExperimentList

    -
    value
    +
    value

    An assay compatible with the MultiAssayExperiment API

    -
    -

    Value

    - - -

    subsetBy* operations are endomorphic and return either +

    +

    Value

    +

    subsetBy* operations are endomorphic and return either MultiAssayExperiment or ExperimentList depending on the input.

    -
    -

    Details

    +
    +

    Details

    Subsetting a MultiAssayExperiment by the j index can yield a call to either subsetByColData or subsetByColumn. For vector inputs, the subset will be applied to the colData rows. For List-type @@ -204,8 +173,8 @@

    Details

  • subsetByAssay: Select experiments

  • -
    -

    Examples

    +
    +

    Examples

    ## Load the example MultiAssayExperiment
     example("MultiAssayExperiment")
     #> 
    @@ -512,27 +481,23 @@ 

    Examples

    -
    - - + -
    +
    + - - diff --git a/reference/subsetByAssay,ExperimentList-method.html b/reference/subsetByAssay,ExperimentList-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByAssay,ExperimentList-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByAssay,MultiAssayExperiment-method.html b/reference/subsetByAssay,MultiAssayExperiment-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByAssay,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByAssay.html b/reference/subsetByAssay.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByAssay.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByColData,MultiAssayExperiment,ANY-method.html b/reference/subsetByColData,MultiAssayExperiment,ANY-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByColData,MultiAssayExperiment,ANY-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByColData,MultiAssayExperiment,character-method.html b/reference/subsetByColData,MultiAssayExperiment,character-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByColData,MultiAssayExperiment,character-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByColData.html b/reference/subsetByColData.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByColData.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByColumn,ExperimentList,List-method.html b/reference/subsetByColumn,ExperimentList,List-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByColumn,ExperimentList,List-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByColumn,ExperimentList,list-method.html b/reference/subsetByColumn,ExperimentList,list-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByColumn,ExperimentList,list-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByColumn,ExperimentList,logical-method.html b/reference/subsetByColumn,ExperimentList,logical-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByColumn,ExperimentList,logical-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByColumn,MultiAssayExperiment,ANY-method.html b/reference/subsetByColumn,MultiAssayExperiment,ANY-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByColumn,MultiAssayExperiment,ANY-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByColumn.html b/reference/subsetByColumn.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByColumn.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByRow,ExperimentList,ANY-method.html b/reference/subsetByRow,ExperimentList,ANY-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByRow,ExperimentList,ANY-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByRow,ExperimentList,List-method.html b/reference/subsetByRow,ExperimentList,List-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByRow,ExperimentList,List-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByRow,ExperimentList,list-method.html b/reference/subsetByRow,ExperimentList,list-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByRow,ExperimentList,list-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByRow,ExperimentList,logical-method.html b/reference/subsetByRow,ExperimentList,logical-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByRow,ExperimentList,logical-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByRow,MultiAssayExperiment,ANY-method.html b/reference/subsetByRow,MultiAssayExperiment,ANY-method.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByRow,MultiAssayExperiment,ANY-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/subsetByRow.html b/reference/subsetByRow.html new file mode 100644 index 00000000..fe463cec --- /dev/null +++ b/reference/subsetByRow.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/updateObject,MultiAssayExperiment-method.html b/reference/updateObject,MultiAssayExperiment-method.html new file mode 100644 index 00000000..56cdeb87 --- /dev/null +++ b/reference/updateObject,MultiAssayExperiment-method.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/upsetSamples-1.png b/reference/upsetSamples-1.png index b3397a51..615844ad 100644 Binary files a/reference/upsetSamples-1.png and b/reference/upsetSamples-1.png differ diff --git a/reference/upsetSamples-2.png b/reference/upsetSamples-2.png index 90908041..c6ebf5fe 100644 Binary files a/reference/upsetSamples-2.png and b/reference/upsetSamples-2.png differ diff --git a/reference/upsetSamples.html b/reference/upsetSamples.html index beb96b9c..94a78d7d 100644 --- a/reference/upsetSamples.html +++ b/reference/upsetSamples.html @@ -1,89 +1,55 @@ -Create a generalized Venn Diagram analog for sample membership in multiple -assays, using the upset algorithm in UpSetR — upsetSamples • MultiAssayExperiment - - -
    -
    -
    - + + +
    +
    +
    +
    -
    +

    Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR

    -
    +
    +

    Usage

    upsetSamples(
       MultiAssayExperiment,
       nsets = NULL,
    @@ -95,63 +61,63 @@ 

    Create a generalized Venn Diagram analog for sample membership in multiple )

    -
    -

    Arguments

    -
    MultiAssayExperiment
    +
    +

    Arguments

    + + +
    MultiAssayExperiment

    A MultiAssayExperiment object

    -
    nsets
    -

    numeric(1) The number of sets to analyze. If specified, +

    nsets
    +

    numeric(1) The number of sets to analyze. If specified, sets will be ignored.

    -
    sets
    -

    character() A character vector of names in MultiAssayExperiment +

    sets
    +

    character() A character vector of names in MultiAssayExperiment to use. If specified, nsets will be ignored.

    -
    nintersects
    -

    numeric() The number of intersections to plot. By +

    nintersects
    +

    numeric(1) The number of intersections to plot. By default, all intersections will be plotted.

    -
    order.by
    +
    order.by

    How the intersections in the matrix should be ordered by. Options include frequency (entered as "freq"), degree, or both in any order.

    -
    check.names
    -

    logical(1) Whether to munge names as in the +

    check.names
    +

    logical(1) Whether to munge names as in the data.frame() constructor (default FALSE).

    -
    ...
    -

    parameters passed to upset

    +
    ...
    +

    parameters passed to UpSetR::upset

    -
    -

    Value

    - - -

    Produces a visualization of set intersections using the UpSet matrix +

    +

    Value

    +

    Produces a visualization of set intersections using the UpSet matrix design

    -
    -

    Note

    +
    +

    Note

    This function is intended to provide convenient visualization of assay availability configurations in MultiAssayExperiment instances. The UpSetR::upset function requires data.frame input and has many parameters to tune appearance of the result. Assay name handling is important for interpretability.

    -
    -

    Author

    +
    +

    Author

    Vincent J Carey

    -
    -

    Examples

    +
    +

    Examples

    
     data(miniACC)
     upsetSamples(miniACC)
    @@ -161,27 +127,23 @@ 

    Examples

    -
    - -
    +
    -
    +
    + - - diff --git a/reference/wideFormat.html b/reference/wideFormat.html new file mode 100644 index 00000000..c21263b9 --- /dev/null +++ b/reference/wideFormat.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/search.json b/search.json new file mode 100644 index 00000000..2e2bb702 --- /dev/null +++ b/search.json @@ -0,0 +1 @@ +[{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Loading packages:","code":"if (!require(\"BiocManager\")) install.packages(\"BiocManager\") BiocManager::install(\"MultiAssayExperiment\") library(MultiAssayExperiment) library(GenomicRanges) library(SummarizedExperiment) library(RaggedExperiment)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"citing-multiassayexperiment","dir":"Articles","previous_headings":"","what":"Citing MultiAssayExperiment","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Without citations free open-source software possible. Please cite MultiAssayExperiment shown References section (Ramos et al. (2017)). may also refer Cancer Research publication AACR Journals link .","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"a-brief-description","dir":"Articles","previous_headings":"","what":"A Brief Description","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"MultiAssayExperiment offers data structure representing analyzing multi-omics experiments: biological analysis approach utilizing multiple types observations, DNA mutations abundance RNA proteins, biological specimens.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"choosing-the-appropriate-data-structure","dir":"Articles","previous_headings":"A Brief Description","what":"Choosing the appropriate data structure","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"assays different numbers rows even columns, MultiAssayExperiment recommended. sets assays information across rows (e.g., genes genomic ranges), SummarizedExperiment recommended data structure.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"overview-of-the-multiassayexperiment-class","dir":"Articles","previous_headings":"","what":"Overview of the MultiAssayExperiment class","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"overview class constructors extractors: visual representation MultiAssayExperiment class accessor functions can seen . three main components: ExperimentList colData sampleMap MultiAssayExperiment object schematic shows design infrastructure class. colData provides data patients, cell lines, biological units, one row per unit one column per variable. experiments list assay datasets arbitrary class, one column per observation. sampleMap links single table patient data (colData) list experiments via simple powerful table experiment:patient edges (relationships), can created automatically simple cases spreadsheet assay-specific sample identifiers used. sampleMap relates column (observation) assays (experiments) exactly one row (biological unit) colData; however, one row colData may map zero, one, columns per assay, allowing missing replicate assays. Green stripes indicate mapping one subject multiple observations across experiments.","code":"empty <- MultiAssayExperiment() empty ## A MultiAssayExperiment object of 0 listed ## experiments with no user-defined names and respective classes. ## Containing an ExperimentList class object of length 0: ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files slotNames(empty) ## [1] \"ExperimentList\" \"colData\" \"sampleMap\" \"drops\" ## [5] \"metadata\""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"experimentlist-experimental-data","dir":"Articles","previous_headings":"Overview of the MultiAssayExperiment class > Components of the MultiAssayExperiment","what":"ExperimentList: experimental data","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"ExperimentList slot class container workhorse MultiAssayExperiment class. contains experimental data. inherits class S4Vectors::SimpleList one element/component per data type. elements ExperimentList can contain ID-based range-based data. Requirements classes ExperimentList listed API. following base Bioconductor classes known work elements ExperimentList: base::matrix: base class, can used ID-based datasets gene expression summarized per-gene, microRNA, metabolomics, microbiome data. SummarizedExperiment::SummarizedExperiment: richer representation compared ordinary matrix ID-based datasets capable storing additional assay- level metadata. Biobase::ExpressionSet: legacy representation ID-based datasets, supported convenience supplanted SummarizedExperiment. SummarizedExperiment::RangedSummarizedExperiment: rectangular range-based datasets, one set genomic ranges assayed multiple samples. can used gene expression, methylation, data types refer genomic positions. RaggedExperiment::RaggedExperiment: range-based datasets, copy number mutation data, RaggedExperiment class can used represent measurements genomic positions.","code":"class(experiments(empty)) # ExperimentList ## [1] \"ExperimentList\" ## attr(,\"package\") ## [1] \"MultiAssayExperiment\""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"class-requirements-within-experimentlist-container","dir":"Articles","previous_headings":"Overview of the MultiAssayExperiment class > Components of the MultiAssayExperiment > ExperimentList: experimental data","what":"Class requirements within ExperimentList container","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"See API section details requirements using data classes. general, data classes meeting minimum requirements, including support square bracket [ subsetting dimnames() work default. datasets contained elements ExperimentList can : column names (required) row names (optional) column names correspond samples, used match assay data specimen metadata stored colData. row names can correspond variety features data including limited gene names, probe IDs, proteins, named ranges. Note existence “row” names mean data must rectangular matrix-like. Classes contained ExperimentList must support following list methods: [: single square bracket subsetting, single comma. assumed values comma subset rows, values comma subset columns. dimnames() : corresponding features (genes, proteins, etc.) experimental samples dim(): returns vector number rows number columns","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"coldata-primary-data","dir":"Articles","previous_headings":"Overview of the MultiAssayExperiment class > Components of the MultiAssayExperiment","what":"colData: primary data","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"MultiAssayExperiment keeps one set “primary” metadata describes ‘biological unit’ can refer specimens, experimental subjects, patients, etc. vignette, refer experimental subject patient.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"coldata-slot-requirements","dir":"Articles","previous_headings":"Overview of the MultiAssayExperiment class > Components of the MultiAssayExperiment > colData: primary data","what":"colData slot requirements","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"colData dataset class DataFrame can accept data.frame class object coerced. order relate metadata biological unit, row names colData dataset must contain patient identifiers. Key points: one row colData can map zero, one, columns ExperimentList element row colData must map least one column least one ExperimentList element. column ExperimentList element must map exactly one row colData. relationships defined sampleMap.","code":"patient.data <- data.frame(sex=c(\"M\", \"F\", \"M\", \"F\"), age=38:41, row.names=c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\")) patient.data ## sex age ## Jack M 38 ## Jill F 39 ## Bob M 40 ## Barbara F 41"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"note-on-the-flexibility-of-the-dataframe","dir":"Articles","previous_headings":"Overview of the MultiAssayExperiment class > Components of the MultiAssayExperiment > colData: primary data","what":"Note on the flexibility of the DataFrame","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"many typical purposes DataFrame data.frame behave equivalently; Dataframe flexible allows vector-like data type stored columns. flexibility DataFrame permits, example, storing multiple dose-response values single cell line, even number doses responses consistent across cell lines. Doses stored one column colData SimpleList, responses another column, also SimpleList. , dose-response values stored single column colData two-column matrix cell line.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"sampleMap","dir":"Articles","previous_headings":"Overview of the MultiAssayExperiment class > Components of the MultiAssayExperiment","what":"sampleMap: relating colData to multiple assays","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"sampleMap DataFrame relates “primary” data (colData) experimental assays: sampleMap provides unambiguous map every experimental observation one one row colData. , however, permissible row colData associated multiple experimental observations observations . words, “many--one” mapping experimental observations rows colData, “one---number” mapping rows colData experimental observations.","code":"is(sampleMap(empty), \"DataFrame\") # TRUE ## [1] TRUE"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"samplemap-structure","dir":"Articles","previous_headings":"Overview of the MultiAssayExperiment class > Components of the MultiAssayExperiment > sampleMap: relating colData to multiple assays","what":"sampleMap structure","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"sampleMap three columns, following column names: assay provides names different experiments / assays performed. user-defined, requirement names ExperimentList, experimental assays stored, must contained column. primary provides “primary” sample names. values column must also present rownames colData(MultiAssayExperiment). example, allowable values column “Jack”, “Jill”, “Barbara”, “Bob”. colname provides sample names used experimental datasets, practice often different primary sample names. assay, column names must found column. Otherwise, assays orphaned: impossible match samples overall experiment. mentioned , duplicate values allowed, represent replicates overall experiment-level annotation. design motivated following situations: allows flexibility amount technical replication biological replication (tumor matched normal single patient) individual assays. allows missing observations (RNA-seq performed patients). allows use different identifiers used patients / specimens assay. different identifiers matched unambiguously, consistency maintained subsetting re-ordering.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"instances-where-samplemap-isnt-provided","dir":"Articles","previous_headings":"","what":"MultiAssayExperiment: The Integrative Bioconductor Container","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"assay uses colnames (.e., sample identifiers used experiment), simple list datasets sufficient MultiAssayExperiment constructor function. necessary rownames colnames: example, user provide colData argument constructor function filled empty DataFrame: colData can provided. , note assay sample (column) mapped corresponding row provided colData gets dropped. part ensuring internal validity MultiAssayExperiment.","code":"exprss1 <- matrix(rnorm(16), ncol = 4, dimnames = list(sprintf(\"ENST00000%i\", sample(288754:290000, 4)), c(\"Jack\", \"Jill\", \"Bob\", \"Bobby\"))) exprss2 <- matrix(rnorm(12), ncol = 3, dimnames = list(sprintf(\"ENST00000%i\", sample(288754:290000, 4)), c(\"Jack\", \"Jane\", \"Bob\"))) doubleExp <- list(\"methyl 2k\" = exprss1, \"methyl 3k\" = exprss2) simpleMultiAssay <- MultiAssayExperiment(experiments=doubleExp) simpleMultiAssay ## A MultiAssayExperiment object of 2 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 2: ## [1] methyl 2k: matrix with 4 rows and 4 columns ## [2] methyl 3k: matrix with 4 rows and 3 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files colData(simpleMultiAssay) ## DataFrame with 5 rows and 0 columns simpleMultiAssay2 <- MultiAssayExperiment(experiments=doubleExp, colData=patient.data) ## Warning: Data dropped from ExperimentList (element - column): ## methyl 2k - Bobby ## methyl 3k - Jane ## Unable to map to rows of colData ## harmonizing input: ## removing 1 colData rownames not in sampleMap 'primary' simpleMultiAssay2 ## A MultiAssayExperiment object of 2 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 2: ## [1] methyl 2k: matrix with 4 rows and 3 columns ## [2] methyl 3k: matrix with 4 rows and 2 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files colData(simpleMultiAssay2) ## DataFrame with 3 rows and 2 columns ## sex age ## ## Jack M 38 ## Jill F 39 ## Bob M 40"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"metadata","dir":"Articles","previous_headings":"Overview of the MultiAssayExperiment class > Components of the MultiAssayExperiment","what":"metadata","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Metadata can added different levels MultiAssayExperiment. Can class, storing study-wide metadata, citation information. empty MultiAssayExperiment object, NULL. ExperimentList level, metadata function allow user enter metadata list. individual assay level, certain classes may support metadata, example, metadata mcols SummarizedExperiment. recommended use metadata ExperimentList level. back top","code":"class(metadata(empty)) # NULL (class \"ANY\") ## [1] \"list\" metadata(experiments(empty)) ## list()"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"creating-a-multiassayexperiment-object-a-rich-example","dir":"Articles","previous_headings":"","what":"Creating a MultiAssayExperiment object: a rich example","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"section demonstrate core supported data classes, using different sample ID conventions assay, primary colData. supported classes , matrix, SummarizedExperiment, RangedSummarizedExperiment.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"create-toy-datasets-demonstrating-all-supported-data-types","dir":"Articles","previous_headings":"Creating a MultiAssayExperiment object: a rich example","what":"Create toy datasets demonstrating all supported data types","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"three matrix-like datasets. First, let’s represent expression data SummarizedExperiment: following map matches colData sample names exprdata sample names. Note row orders aren’t initially matched , OK. Now methylation data, represent matrix. uses gene identifiers also, measures partially overlapping set genes. Now, let’s store simple matrix can contains replicate one patients. following map matches colData sample names methyldat sample names. Now microRNA platform, common identifiers datasets, also represent matrix. also missing data “Jill”. use sample naming convention arrays. following map matches colData sample names microdat sample names. Finally, create dataset class RangedSummarizedExperiment: map colData samples RangedSummarizedExperiment:","code":"(arraydat <- matrix(seq(101, 108), ncol=4, dimnames=list(c(\"ENST00000294241\", \"ENST00000355076\"), c(\"array1\", \"array2\", \"array3\", \"array4\")))) ## array1 array2 array3 array4 ## ENST00000294241 101 103 105 107 ## ENST00000355076 102 104 106 108 coldat <- data.frame(slope53=rnorm(4), row.names=c(\"array1\", \"array2\", \"array3\", \"array4\")) exprdat <- SummarizedExperiment(arraydat, colData=coldat) exprdat ## class: SummarizedExperiment ## dim: 2 4 ## metadata(0): ## assays(1): '' ## rownames(2): ENST00000294241 ENST00000355076 ## rowData names(0): ## colnames(4): array1 array2 array3 array4 ## colData names(1): slope53 (exprmap <- data.frame(primary=rownames(patient.data)[c(1, 2, 4, 3)], colname=c(\"array1\", \"array2\", \"array3\", \"array4\"), stringsAsFactors = FALSE)) ## primary colname ## 1 Jack array1 ## 2 Jill array2 ## 3 Barbara array3 ## 4 Bob array4 (methyldat <- matrix(1:10, ncol=5, dimnames=list(c(\"ENST00000355076\", \"ENST00000383706\"), c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\")))) ## methyl1 methyl2 methyl3 methyl4 methyl5 ## ENST00000355076 1 3 5 7 9 ## ENST00000383706 2 4 6 8 10 (methylmap <- data.frame(primary = c(\"Jack\", \"Jack\", \"Jill\", \"Barbara\", \"Bob\"), colname = c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\"), stringsAsFactors = FALSE)) ## primary colname ## 1 Jack methyl1 ## 2 Jack methyl2 ## 3 Jill methyl3 ## 4 Barbara methyl4 ## 5 Bob methyl5 (microdat <- matrix(201:212, ncol=3, dimnames=list(c(\"hsa-miR-21\", \"hsa-miR-191\", \"hsa-miR-148a\", \"hsa-miR148b\"), c(\"micro1\", \"micro2\", \"micro3\")))) ## micro1 micro2 micro3 ## hsa-miR-21 201 205 209 ## hsa-miR-191 202 206 210 ## hsa-miR-148a 203 207 211 ## hsa-miR148b 204 208 212 (micromap <- data.frame(primary = c(\"Jack\", \"Barbara\", \"Bob\"), colname = c(\"micro1\", \"micro2\", \"micro3\"), stringsAsFactors = FALSE)) ## primary colname ## 1 Jack micro1 ## 2 Barbara micro2 ## 3 Bob micro3 nrows <- 5; ncols <- 4 counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows) rowRanges <- GRanges(rep(c(\"chr1\", \"chr2\"), c(2, nrows - 2)), IRanges(floor(runif(nrows, 1e5, 1e6)), width=100), strand=sample(c(\"+\", \"-\"), nrows, TRUE), feature_id=sprintf(\"ID\\\\%03d\", 1:nrows)) names(rowRanges) <- letters[1:5] colData <- DataFrame(Treatment=rep(c(\"ChIP\", \"Input\"), 2), row.names= c(\"mysnparray1\", \"mysnparray2\", \"mysnparray3\", \"mysnparray4\")) rse <- SummarizedExperiment(assays=SimpleList(counts=counts), rowRanges=rowRanges, colData=colData) (rangemap <- data.frame(primary = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\"), colname = c(\"mysnparray1\", \"mysnparray2\", \"mysnparray3\", \"mysnparray4\"), stringsAsFactors = FALSE)) ## primary colname ## 1 Jack mysnparray1 ## 2 Jill mysnparray2 ## 3 Bob mysnparray3 ## 4 Barbara mysnparray4"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"samplemap-creation","dir":"Articles","previous_headings":"Creating a MultiAssayExperiment object: a rich example","what":"sampleMap creation","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"MultiAssayExperiment constructor function can create sampleMap automatically single naming convention used, example used platform-specific sample identifiers (e.g. mysnparray1, etc). must provide ID map matches samples experiment back colData, three-column data.frame DataFrame three columns named “assay”, primary”, “colname”. start list: use convenience function listToMap convert list data.frame objects valid object sampleMap: Note, dfmap can reverted list another provided function:","code":"listmap <- list(exprmap, methylmap, micromap, rangemap) names(listmap) <- c(\"Affy\", \"Methyl 450k\", \"Mirna\", \"CNV gistic\") listmap ## $Affy ## primary colname ## 1 Jack array1 ## 2 Jill array2 ## 3 Barbara array3 ## 4 Bob array4 ## ## $`Methyl 450k` ## primary colname ## 1 Jack methyl1 ## 2 Jack methyl2 ## 3 Jill methyl3 ## 4 Barbara methyl4 ## 5 Bob methyl5 ## ## $Mirna ## primary colname ## 1 Jack micro1 ## 2 Barbara micro2 ## 3 Bob micro3 ## ## $`CNV gistic` ## primary colname ## 1 Jack mysnparray1 ## 2 Jill mysnparray2 ## 3 Bob mysnparray3 ## 4 Barbara mysnparray4 dfmap <- listToMap(listmap) dfmap ## DataFrame with 16 rows and 3 columns ## assay primary colname ## ## 1 Affy Jack array1 ## 2 Affy Jill array2 ## 3 Affy Barbara array3 ## 4 Affy Bob array4 ## 5 Methyl 450k Jack methyl1 ## ... ... ... ... ## 12 Mirna Bob micro3 ## 13 CNV gistic Jack mysnparray1 ## 14 CNV gistic Jill mysnparray2 ## 15 CNV gistic Bob mysnparray3 ## 16 CNV gistic Barbara mysnparray4 mapToList(dfmap, \"assay\")"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"experimental-data-as-a-list","dir":"Articles","previous_headings":"Creating a MultiAssayExperiment object: a rich example","what":"Experimental data as a list()","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Create named list experiments MultiAssayExperiment function. names must found within third column dfmap:","code":"objlist <- list(\"Affy\" = exprdat, \"Methyl 450k\" = methyldat, \"Mirna\" = microdat, \"CNV gistic\" = rse)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"creation-of-the-multiassayexperiment-class-object","dir":"Articles","previous_headings":"Creating a MultiAssayExperiment object: a rich example","what":"Creation of the MultiAssayExperiment class object","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"recommend using MultiAssayExperiment constructor function: following extractor functions can used get extract data object: Note ExperimentList class extends SimpleList class add validity checks specific MultiAssayExperiment. can used like list.","code":"myMultiAssay <- MultiAssayExperiment(objlist, patient.data, dfmap) myMultiAssay ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 4 columns ## [2] Methyl 450k: matrix with 2 rows and 5 columns ## [3] Mirna: matrix with 4 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files experiments(myMultiAssay) ## ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 4 columns ## [2] Methyl 450k: matrix with 2 rows and 5 columns ## [3] Mirna: matrix with 4 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns colData(myMultiAssay) ## DataFrame with 4 rows and 2 columns ## sex age ## ## Jack M 38 ## Jill F 39 ## Bob M 40 ## Barbara F 41 sampleMap(myMultiAssay) ## DataFrame with 16 rows and 3 columns ## assay primary colname ## ## 1 Affy Jack array1 ## 2 Affy Jill array2 ## 3 Affy Barbara array3 ## 4 Affy Bob array4 ## 5 Methyl 450k Jack methyl1 ## ... ... ... ... ## 12 Mirna Bob micro3 ## 13 CNV gistic Jack mysnparray1 ## 14 CNV gistic Jill mysnparray2 ## 15 CNV gistic Bob mysnparray3 ## 16 CNV gistic Barbara mysnparray4 metadata(myMultiAssay) ## list()"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"helper-function-to-create-a-multiassayexperiment-object","dir":"Articles","previous_headings":"Creating a MultiAssayExperiment object: a rich example","what":"Helper function to create a MultiAssayExperiment object","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"prepMultiAssay function helps diagnose common problems creating MultiAssayExperiment object. provides error messages /warnings instances names (either colnames ExperimentList element names) inconsistent found sampleMap. Input arguments MultiAssayExperiment (.e., ExperimentList, colData, sampleMap). resulting output prepMultiAssay function list inputs including “metadata$drops” element names able matched. Instances ExperimentList created without names prompt error prepMultiAssay. Named ExperimentList elements essential checks MultiAssayExperiment. Non-matching names may also present ExperimentList elements “assay” column sampleMap. names differ case identical unique, names standardized lower case replaced. colnames ExperimentList matched back primary data (colData), dropped added drops element. similar operation performed checking “primary” sampleMap names colData rownames. example, add row corresponding “Joe” match experimental data. create MultiAssayExperiment results prepMultiAssay function, take corresponding element resulting list enter arguments MultiAssayExperiment constructor function. Alternatively, use .call function easily create MultiAssayExperiment output prepMultiAssay function:","code":"objlist3 <- objlist (names(objlist3) <- NULL) ## NULL try(prepMultiAssay(objlist3, patient.data, dfmap)$experiments, outFile = stdout()) ## Error in prepMultiAssay(objlist3, patient.data, dfmap) : ## ExperimentList does not have names, assign names names(objlist3) <- toupper(names(objlist)) names(objlist3) ## [1] \"AFFY\" \"METHYL 450K\" \"MIRNA\" \"CNV GISTIC\" unique(dfmap[, \"assay\"]) ## [1] Affy Methyl 450k Mirna CNV gistic ## Levels: Affy Methyl 450k Mirna CNV gistic prepMultiAssay(objlist3, patient.data, dfmap)$experiments ## ## Names in the ExperimentList do not match sampleMap assay ## standardizing will be attempted... ## - names set to lowercase ## ExperimentList class object of length 4: ## [1] affy: SummarizedExperiment with 2 rows and 4 columns ## [2] methyl 450k: matrix with 2 rows and 5 columns ## [3] mirna: matrix with 4 rows and 3 columns ## [4] cnv gistic: RangedSummarizedExperiment with 5 rows and 4 columns exampleMap <- sampleMap(simpleMultiAssay2) sapply(doubleExp, colnames) ## $`methyl 2k` ## [1] \"Jack\" \"Jill\" \"Bob\" \"Bobby\" ## ## $`methyl 3k` ## [1] \"Jack\" \"Jane\" \"Bob\" exampleMap ## DataFrame with 5 rows and 3 columns ## assay primary colname ## ## 1 methyl 2k Jack Jack ## 2 methyl 2k Jill Jill ## 3 methyl 2k Bob Bob ## 4 methyl 3k Jack Jack ## 5 methyl 3k Bob Bob prepMultiAssay(doubleExp, patient.data, exampleMap)$metadata$drops ## ## Not all colnames in the ExperimentList are found in the ## sampleMap, dropping samples from ExperimentList... ## $`methyl 2k` ## [1] \"Bobby\" ## ## $`methyl 3k` ## [1] \"Jane\" ## $`columns.methyl 2k` ## [1] \"Bobby\" ## ## $`columns.methyl 3k` ## [1] \"Jane\" exMap <- rbind(dfmap, DataFrame(assay = \"New methyl\", primary = \"Joe\", colname = \"Joe\")) invisible(prepMultiAssay(objlist, patient.data, exMap)) ## Warning in prepMultiAssay(objlist, patient.data, exMap): ## Lengths of names in the ExperimentList and sampleMap ## are not equal ## ## Not all names in the primary column of the sampleMap ## could be matched to the colData rownames; see $drops ## DataFrame with 1 row and 3 columns ## assay primary colname ## ## 1 New methyl Joe Joe prepped <- prepMultiAssay(objlist, patient.data, exMap) ## Warning in prepMultiAssay(objlist, patient.data, exMap): ## Lengths of names in the ExperimentList and sampleMap ## are not equal ## ## Not all names in the primary column of the sampleMap ## could be matched to the colData rownames; see $drops ## DataFrame with 1 row and 3 columns ## assay primary colname ## ## 1 New methyl Joe Joe preppedMulti <- MultiAssayExperiment(prepped$experiments, prepped$colData, prepped$sampleMap, prepped$metadata) preppedMulti ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 4 columns ## [2] Methyl 450k: matrix with 2 rows and 5 columns ## [3] Mirna: matrix with 4 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files do.call(MultiAssayExperiment, prepped) ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 4 columns ## [2] Methyl 450k: matrix with 2 rows and 5 columns ## [3] Mirna: matrix with 4 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"helper-functions-to-create-bioconductor-classes-from-raw-data","dir":"Articles","previous_headings":"Creating a MultiAssayExperiment object: a rich example","what":"Helper functions to create Bioconductor classes from raw data","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Recent updates GenomicRanges SummarizedExperiment packages allow user create standard Bioconductor classes raw data. Raw data read either data.frame DataFrame can converted GRangesList SummarizedExperiment classes depending type data. function create GRangesList data.frame, called makeGRangesListFromDataFrame can found GenomicRanges package. makeSummarizedExperimentFromDataFrame available SummarizedExperiment package. also possible create RangedSummarizedExperiment class object raw data ranged data available. simple example can obtained function documentation GenomicRanges: can converted RaggedExperiment object rectangular representation conform easily MultiAssayExperiment API requirements. Note. See RaggedExperiment vignette details. SummarizedExperiment package: back top","code":"grlls <- list(chr = rep(\"chr1\", nrows), start = seq(11, 15), end = seq(12, 16), strand = c(\"+\", \"-\", \"+\", \"*\", \"*\"), score = seq(1, 5), specimen = c(\"a\", \"a\", \"b\", \"b\", \"c\"), gene_symbols = paste0(\"GENE\", letters[seq_len(nrows)])) grldf <- as.data.frame(grlls, stringsAsFactors = FALSE) GRL <- makeGRangesListFromDataFrame(grldf, split.field = \"specimen\", names.field = \"gene_symbols\") RaggedExperiment(GRL) ## class: RaggedExperiment ## dim: 5 3 ## assays(0): ## rownames(5): GENEa GENEb GENEc GENEd GENEe ## colnames(3): a b c ## colData names(0): sels <- list(chr = rep(\"chr2\", nrows), start = seq(11, 15), end = seq(12, 16), strand = c(\"+\", \"-\", \"+\", \"*\", \"*\"), expr0 = seq(3, 7), expr1 = seq(8, 12), expr2 = seq(12, 16)) sedf <- as.data.frame(sels, row.names = paste0(\"GENE\", letters[rev(seq_len(nrows))]), stringsAsFactors = FALSE) sedf ## chr start end strand expr0 expr1 expr2 ## GENEe chr2 11 12 + 3 8 12 ## GENEd chr2 12 13 - 4 9 13 ## GENEc chr2 13 14 + 5 10 14 ## GENEb chr2 14 15 * 6 11 15 ## GENEa chr2 15 16 * 7 12 16 makeSummarizedExperimentFromDataFrame(sedf) ## class: RangedSummarizedExperiment ## dim: 5 3 ## metadata(0): ## assays(1): '' ## rownames(5): GENEe GENEd GENEc GENEb GENEa ## rowData names(0): ## colnames(3): expr0 expr1 expr2 ## colData names(0):"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"integrated-subsetting-across-experiments","dir":"Articles","previous_headings":"","what":"Integrated subsetting across experiments","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"MultiAssayExperiment allows subsetting rows, columns, assays, rownames, colnames, across experiments simultaneously guaranteeing continued matching samples. Subsetting can done compactly square bracket method, verbosely potentially flexibly subsetBy*() methods.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"subsetting-by-square-bracket","dir":"Articles","previous_headings":"Integrated subsetting across experiments","what":"Subsetting by square bracket [","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"three positions within bracket operator indicate rows, columns, assays, respectively (pseudocode): example, select gene “ENST00000355076”: operation works across types assays, whether ID-based (e.g. matrix, ExpressionSet, SummarizedExperiment) range-based (e.g. RangedSummarizedExperiment). Note using bracket method [, drop argument TRUE default. can subset rows, columns, assays single bracket operation, performed order (rows, columns, assays). following selects ENST00000355076 gene across samples, first two samples assay, finally Affy Methyl 450k assays:","code":"myMultiAssay[rows, columns, assays] myMultiAssay[\"ENST00000355076\", , ] ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 1 rows and 4 columns ## [2] Methyl 450k: matrix with 1 rows and 5 columns ## [3] Mirna: matrix with 0 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 0 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files myMultiAssay[\"ENST00000355076\", 1:2, c(\"Affy\", \"Methyl 450k\")] ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 3 sampleMap rows not in names(experiments) ## A MultiAssayExperiment object of 2 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 2: ## [1] Affy: SummarizedExperiment with 1 rows and 2 columns ## [2] Methyl 450k: matrix with 1 rows and 3 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"subsetting-by-character-integer-and-logical","dir":"Articles","previous_headings":"Integrated subsetting across experiments","what":"Subsetting by character, integer, and logical","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"columns - character, integer, logical allowed, example: assay - character, integer, logical allowed:","code":"myMultiAssay[, \"Jack\", ] ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 1 columns ## [2] Methyl 450k: matrix with 2 rows and 2 columns ## [3] Mirna: matrix with 4 rows and 1 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 1 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files myMultiAssay[, 1, ] ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 1 columns ## [2] Methyl 450k: matrix with 2 rows and 2 columns ## [3] Mirna: matrix with 4 rows and 1 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 1 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files myMultiAssay[, c(TRUE, FALSE, FALSE, FALSE), ] ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 1 columns ## [2] Methyl 450k: matrix with 2 rows and 2 columns ## [3] Mirna: matrix with 4 rows and 1 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 1 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files myMultiAssay[, , \"Mirna\"] ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 13 sampleMap rows not in names(experiments) ## removing 1 colData rownames not in sampleMap 'primary' ## A MultiAssayExperiment object of 1 listed ## experiment with a user-defined name and respective class. ## Containing an ExperimentList class object of length 1: ## [1] Mirna: matrix with 4 rows and 3 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files myMultiAssay[, , 3] ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 13 sampleMap rows not in names(experiments) ## removing 1 colData rownames not in sampleMap 'primary' ## A MultiAssayExperiment object of 1 listed ## experiment with a user-defined name and respective class. ## Containing an ExperimentList class object of length 1: ## [1] Mirna: matrix with 4 rows and 3 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files myMultiAssay[, , c(FALSE, FALSE, TRUE, FALSE, FALSE)] ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 13 sampleMap rows not in names(experiments) ## removing 1 colData rownames not in sampleMap 'primary' ## A MultiAssayExperiment object of 1 listed ## experiment with a user-defined name and respective class. ## Containing an ExperimentList class object of length 1: ## [1] Mirna: matrix with 4 rows and 3 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"the-drop-argument","dir":"Articles","previous_headings":"Integrated subsetting across experiments","what":"the “drop” argument","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Specify drop=FALSE keep assays zero rows zero columns, e.g.: Using default drop=TRUE, assays rows columns removed:","code":"myMultiAssay[\"ENST00000355076\", , , drop=FALSE] ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 1 rows and 4 columns ## [2] Methyl 450k: matrix with 1 rows and 5 columns ## [3] Mirna: matrix with 0 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 0 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files myMultiAssay[\"ENST00000355076\", , , drop=TRUE] ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 7 sampleMap rows not in names(experiments) ## A MultiAssayExperiment object of 2 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 2: ## [1] Affy: SummarizedExperiment with 1 rows and 4 columns ## [2] Methyl 450k: matrix with 1 rows and 5 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"more-on-subsetting-by-columns","dir":"Articles","previous_headings":"Integrated subsetting across experiments","what":"More on subsetting by columns","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Experimental samples stored rows colData columns elements ExperimentList, refer subsetting columns, referring columns experimental assays. Subsetting samples / columns obvious recalling colData: Subsetting samples identifies selected samples rows colData DataFrame, selects columns ExperimentList corresponding rows. use integer keep first two rows colData, experimental assays associated two primary samples: Note operation keeps different numbers columns / samples assay, reflecting reality samples may assayed experiments, may replicates . Columns can subset using logical vector. dollar sign operator ($) accesses one columns colData. Finally, special use cases can exert detailed control row column subsetting, using list CharacterList subset. following creates CharacterList column names assay: Now let’s get rid three Methyl 450k arrays, positions 3, 4, 5:","code":"colData(myMultiAssay) ## DataFrame with 4 rows and 2 columns ## sex age ## ## Jack M 38 ## Jill F 39 ## Bob M 40 ## Barbara F 41 myMultiAssay[, 1:2] ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 2 columns ## [2] Methyl 450k: matrix with 2 rows and 3 columns ## [3] Mirna: matrix with 4 rows and 1 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 2 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files malesMultiAssay <- myMultiAssay[, myMultiAssay$sex == \"M\"] colData(malesMultiAssay) ## DataFrame with 2 rows and 2 columns ## sex age ## ## Jack M 38 ## Bob M 40 allsamples <- colnames(myMultiAssay) allsamples ## CharacterList of length 4 ## [[\"Affy\"]] array1 array2 array3 array4 ## [[\"Methyl 450k\"]] methyl1 methyl2 methyl3 methyl4 methyl5 ## [[\"Mirna\"]] micro1 micro2 micro3 ## [[\"CNV gistic\"]] mysnparray1 mysnparray2 mysnparray3 mysnparray4 allsamples[[\"Methyl 450k\"]] <- allsamples[[\"Methyl 450k\"]][-3:-5] myMultiAssay[, as.list(allsamples), ] ## harmonizing input: ## removing 3 sampleMap rows with 'colname' not in colnames of experiments ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 4 columns ## [2] Methyl 450k: matrix with 2 rows and 2 columns ## [3] Mirna: matrix with 4 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files subsetByColumn(myMultiAssay, as.list(allsamples)) #equivalent ## harmonizing input: ## removing 3 sampleMap rows with 'colname' not in colnames of experiments ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 4 columns ## [2] Methyl 450k: matrix with 2 rows and 2 columns ## [3] Mirna: matrix with 4 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"subsetting-assays","dir":"Articles","previous_headings":"Integrated subsetting across experiments","what":"Subsetting assays","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"can select certain assays / experiments using subset, providing character, logical, integer vector. example using character: can subset assays also using logical integer vectors:","code":"myMultiAssay[, , c(\"Affy\", \"CNV gistic\")] ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 8 sampleMap rows not in names(experiments) ## A MultiAssayExperiment object of 2 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 2: ## [1] Affy: SummarizedExperiment with 2 rows and 4 columns ## [2] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files is.cnv <- grepl(\"CNV\", names(experiments(myMultiAssay))) is.cnv ## [1] FALSE FALSE FALSE TRUE myMultiAssay[, , is.cnv] #logical subsetting ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 12 sampleMap rows not in names(experiments) ## A MultiAssayExperiment object of 1 listed ## experiment with a user-defined name and respective class. ## Containing an ExperimentList class object of length 1: ## [1] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files myMultiAssay[, , which(is.cnv)] #integer subsetting ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 12 sampleMap rows not in names(experiments) ## A MultiAssayExperiment object of 1 listed ## experiment with a user-defined name and respective class. ## Containing an ExperimentList class object of length 1: ## [1] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"subsetting-rows-features-by-ids-integers-or-logicals","dir":"Articles","previous_headings":"Integrated subsetting across experiments","what":"Subsetting rows (features) by IDs, integers, or logicals","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Rows assays correspond assay features measurements, genes. Regardless whether assay ID-based (e.g., matrix, ExpressionSet) range-based (e.g., RangedSummarizedExperiment), can subset using following: character vector IDs matched rownames assay integer vector select rows position assay. probably doesn’t make sense unless every ExperimentList element represents measurements order generate error integer elements exceeds number rows ExperimentList element. likely use integer subsetting head function, example look first 6 rows assay. logical vector passed directly row subsetting operation assay. list List element names matching ExperimentList. element subsetting list passed exactly subset rows corresponding element ExperimentList. list List input allows selective subsetting. subsetting applied matching element names ExperimentList. example, take first two rows microRNA dataset, use named list indicate element want subset along drop = FALSE argument. , operations always return MultiAssayExperiment class, unless drop=TRUE passed [ backet subset, ExperimentList element containing feature zero rows. example, return MultiAssayExperiment Affy Methyl 450k contain “ENST0000035076”” row, “Mirna” “CNV gistic” zero rows (drop argument set FALSE default subsetBy*): following, Affy SummarizedExperiment keeps rows order reversed, Methyl 450k keeps second row.","code":"myMultiAssay[list(Mirna = 1:2), , ] ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 4 columns ## [2] Methyl 450k: matrix with 2 rows and 5 columns ## [3] Mirna: matrix with 2 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files ## equivalently subsetByRow(myMultiAssay, list(Mirna = 1:2)) ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 4 columns ## [2] Methyl 450k: matrix with 2 rows and 5 columns ## [3] Mirna: matrix with 2 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files featSub0 <- subsetByRow(myMultiAssay, \"ENST00000355076\") featSub1 <- myMultiAssay[\"ENST00000355076\", , drop = FALSE] #equivalent all.equal(featSub0, featSub1) ## [1] TRUE class(featSub1) ## [1] \"MultiAssayExperiment\" ## attr(,\"package\") ## [1] \"MultiAssayExperiment\" class(experiments(featSub1)) ## [1] \"ExperimentList\" ## attr(,\"package\") ## [1] \"MultiAssayExperiment\" experiments(featSub1) ## ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 1 rows and 4 columns ## [2] Methyl 450k: matrix with 1 rows and 5 columns ## [3] Mirna: matrix with 0 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 0 rows and 4 columns featSubsetted <- subsetByRow(myMultiAssay, c(\"ENST00000355076\", \"ENST00000294241\")) assay(myMultiAssay, 1L) ## array1 array2 array3 array4 ## ENST00000294241 101 103 105 107 ## ENST00000355076 102 104 106 108 assay(featSubsetted, 1L) ## array1 array2 array3 array4 ## ENST00000355076 102 104 106 108 ## ENST00000294241 101 103 105 107"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"subsetting-rows-features-by-genomicranges","dir":"Articles","previous_headings":"Integrated subsetting across experiments","what":"Subsetting rows (features) by GenomicRanges","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"MultiAssayExperiment objects containing range-based objects (currently RangedSummarizedExperiment), can subset using GRanges object, example: Now subsetting. function work IRanges::subsetByOverlaps - see arguments flexible types subsetting range. first three arguments subset, rest passed IRanges::subsetByOverlaps “…”: Square bracket subsetting can still used , passing arguments IRanges::subsetByOverlaps “…” simpler using subsetByRow().","code":"gr <- GRanges(seqnames = c(\"chr1\", \"chr1\", \"chr2\"), strand = c(\"-\", \"+\", \"+\"), ranges = IRanges(start = c(230602, 443625, 934533), end = c(330701, 443724, 934632))) subsetted <- subsetByRow(myMultiAssay, gr, maxgap = 2L, type = \"within\") experiments(subsetted) ## ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 0 rows and 4 columns ## [2] Methyl 450k: matrix with 0 rows and 5 columns ## [3] Mirna: matrix with 0 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 1 rows and 4 columns rowRanges(subsetted[[4]]) ## GRanges object with 1 range and 1 metadata column: ## seqnames ranges strand | feature_id ## | ## a chr1 317182-317281 - | ID\\\\001 ## ------- ## seqinfo: 2 sequences from an unspecified genome; no seqlengths"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"subsetting-is-endomorphic","dir":"Articles","previous_headings":"Integrated subsetting across experiments","what":"Subsetting is endomorphic","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"subsetByRow, subsetByColumn, subsetByAssay, square bracket subsetting “endomorphic” operations, always return another MultiAssayExperiment object.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"double-bracket-subsetting-to-select-experiments","dir":"Articles","previous_headings":"Integrated subsetting across experiments","what":"Double-bracket subsetting to select experiments","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"double-bracket subset operation refers experiment, return object contained within ExperimentList element. endomorphic. example, first ExperimentList element called “Affy” contains SummarizedExperiment: back top","code":"names(myMultiAssay) ## [1] \"Affy\" \"Methyl 450k\" \"Mirna\" \"CNV gistic\" myMultiAssay[[1]] ## class: SummarizedExperiment ## dim: 2 4 ## metadata(0): ## assays(1): '' ## rownames(2): ENST00000294241 ENST00000355076 ## rowData names(0): ## colnames(4): array1 array2 array3 array4 ## colData names(1): slope53 myMultiAssay[[\"Affy\"]] ## class: SummarizedExperiment ## dim: 2 4 ## metadata(0): ## assays(1): '' ## rownames(2): ENST00000294241 ENST00000355076 ## rowData names(0): ## colnames(4): array1 array2 array3 array4 ## colData names(1): slope53"},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"complete-cases","dir":"Articles","previous_headings":"Helpers for data clean-up and management","what":"complete.cases","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"complete.cases function returns logical vector colData rows identifying primary units data experiments. Recall myMultiAssay provides data four individuals: , Jack data 5 experiments: four complete cases Affy Methyl 450k: output can used select individuals complete data:","code":"colData(myMultiAssay) ## DataFrame with 4 rows and 2 columns ## sex age ## ## Jack M 38 ## Jill F 39 ## Bob M 40 ## Barbara F 41 complete.cases(myMultiAssay) ## [1] TRUE FALSE TRUE TRUE complete.cases(myMultiAssay[, , 1:2]) ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 7 sampleMap rows not in names(experiments) ## [1] TRUE TRUE TRUE TRUE myMultiAssay[, complete.cases(myMultiAssay), ] ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 3 columns ## [2] Methyl 450k: matrix with 2 rows and 4 columns ## [3] Mirna: matrix with 4 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 3 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"replicated","dir":"Articles","previous_headings":"Helpers for data clean-up and management","what":"replicated","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"replicated function identifies primary column values biological units multiple observations per assay. returns list LogicalLists indicate biological units one replicate measurements. output used merging replicates default.","code":"replicated(myMultiAssay) ## $Affy ## LogicalList of length 4 ## [[\"Barbara\"]] FALSE FALSE FALSE FALSE ## [[\"Bob\"]] FALSE FALSE FALSE FALSE ## [[\"Jack\"]] FALSE FALSE FALSE FALSE ## [[\"Jill\"]] FALSE FALSE FALSE FALSE ## ## $`Methyl 450k` ## LogicalList of length 4 ## [[\"Barbara\"]] FALSE FALSE FALSE FALSE FALSE ## [[\"Bob\"]] FALSE FALSE FALSE FALSE FALSE ## [[\"Jack\"]] TRUE TRUE FALSE FALSE FALSE ## [[\"Jill\"]] FALSE FALSE FALSE FALSE FALSE ## ## $Mirna ## LogicalList of length 3 ## [[\"Barbara\"]] FALSE FALSE FALSE ## [[\"Bob\"]] FALSE FALSE FALSE ## [[\"Jack\"]] FALSE FALSE FALSE ## ## $`CNV gistic` ## LogicalList of length 4 ## [[\"Barbara\"]] FALSE FALSE FALSE FALSE ## [[\"Bob\"]] FALSE FALSE FALSE FALSE ## [[\"Jack\"]] FALSE FALSE FALSE FALSE ## [[\"Jill\"]] FALSE FALSE FALSE FALSE"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"intersectrows","dir":"Articles","previous_headings":"Helpers for data clean-up and management","what":"intersectRows","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"intersectRows function takes common rownames across experiments returns MultiAssayExperiment rows.","code":"(ensmblMatches <- intersectRows(myMultiAssay[, , 1:2])) ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 7 sampleMap rows not in names(experiments) ## A MultiAssayExperiment object of 2 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 2: ## [1] Affy: SummarizedExperiment with 1 rows and 4 columns ## [2] Methyl 450k: matrix with 1 rows and 5 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files rownames(ensmblMatches) ## CharacterList of length 2 ## [[\"Affy\"]] ENST00000355076 ## [[\"Methyl 450k\"]] ENST00000355076"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"intersectcolumns","dir":"Articles","previous_headings":"Helpers for data clean-up and management","what":"intersectColumns","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"call intersectColumns returns another MultiAssayExperiment columns element ExperimentList correspond exactly rows colData. many cases, operation returns 1--1 correspondence samples patients experiment assay unless replicates present data.","code":"intersectColumns(myMultiAssay) ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 3 columns ## [2] Methyl 450k: matrix with 2 rows and 4 columns ## [3] Mirna: matrix with 4 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 3 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"mergereplicates","dir":"Articles","previous_headings":"Helpers for data clean-up and management","what":"mergeReplicates","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"mergeReplicates function allows user specify function (default: mean) combining replicate columns assay element. can combined intersectColumns create MultiAssayExperiment object one measurement experiment per biological unit.","code":"mergeReplicates(intersectColumns(myMultiAssay)) ## harmonizing input: ## removing 1 sampleMap rows with 'colname' not in colnames of experiments ## A MultiAssayExperiment object of 4 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 4: ## [1] Affy: SummarizedExperiment with 2 rows and 3 columns ## [2] Methyl 450k: matrix with 2 rows and 3 columns ## [3] Mirna: matrix with 4 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 3 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"combine-c","dir":"Articles","previous_headings":"Helpers for data clean-up and management","what":"combine c","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"combine c function allows user append experiment list experiments already present MultiAssayExperiment. case additional observations set samples performed, c function can conveniently referenced existing assay contains ordering sample measurements. mapFrom argument indicates experiment exact organization samples introduced new experiment dataset. number columns new experiment match reference experiment, error thrown. introduce toy dataset created fly: Note: Alternatively, sampleMap additional dataset can provided. back top","code":"c(myMultiAssay, ExpScores = matrix(1:8, ncol = 4, dim = list(c(\"ENSMBL0001\", \"ENSMBL0002\"), paste0(\"pt\", 1:4))), mapFrom = 1L) ## Warning: Assuming column order in the data provided ## matches the order in 'mapFrom' experiment(s) colnames ## A MultiAssayExperiment object of 5 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 5: ## [1] Affy: SummarizedExperiment with 2 rows and 4 columns ## [2] Methyl 450k: matrix with 2 rows and 5 columns ## [3] Mirna: matrix with 4 rows and 3 columns ## [4] CNV gistic: RangedSummarizedExperiment with 5 rows and 4 columns ## [5] ExpScores: matrix with 2 rows and 4 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"extractor-functions","dir":"Articles","previous_headings":"","what":"Extractor functions","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Extractor functions convert MultiAssayExperiment forms convenient analyzing. normally called desired subsetting performed.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"getwithcoldata","dir":"Articles","previous_headings":"Extractor functions","what":"getWithColData","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Provides single assay along associated ‘colData’ columns keeping assay class constant. error target data class support colData replacement method, meaning typically works SummarizedExperiment RaggedExperiment assays extensions.","code":"(affex <- getWithColData(myMultiAssay, 1L)) ## Warning: 'experiments' dropped; see 'drops()' ## class: SummarizedExperiment ## dim: 2 4 ## metadata(0): ## assays(1): '' ## rownames(2): ENST00000294241 ENST00000355076 ## rowData names(0): ## colnames(4): array1 array2 array3 array4 ## colData names(3): slope53 sex age colData(affex) ## DataFrame with 4 rows and 3 columns ## slope53 sex age ## ## array1 0.106685 M 38 ## array2 -0.587014 F 39 ## array3 -0.327854 F 41 ## array4 -0.085361 M 40 class(affex) ## [1] \"SummarizedExperiment\" ## attr(,\"package\") ## [1] \"SummarizedExperiment\""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"longformat-wideformat","dir":"Articles","previous_headings":"Extractor functions","what":"longFormat & wideFormat","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"Produces long (default) wide DataFrame objects. following produces long DataFrame (default) first two assays: especially useful performing regression patient sample data colData using pDataCols argument: “wide” format useful calculating correlations performing regression different genomic features. Wide format general possible replicate measurements, demonstrate cleaned MultiAssayExperiment first 5 columns:","code":"longFormat(myMultiAssay[, , 1:2]) ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 7 sampleMap rows not in names(experiments) ## DataFrame with 18 rows and 5 columns ## assay primary rowname colname value ## ## 1 Affy Jack ENST00000294241 array1 101 ## 2 Affy Jack ENST00000355076 array1 102 ## 3 Affy Jill ENST00000294241 array2 103 ## 4 Affy Jill ENST00000355076 array2 104 ## 5 Affy Barbara ENST00000294241 array3 105 ## ... ... ... ... ... ... ## 14 Methyl 450k Jill ENST00000383706 methyl3 6 ## 15 Methyl 450k Barbara ENST00000355076 methyl4 7 ## 16 Methyl 450k Barbara ENST00000383706 methyl4 8 ## 17 Methyl 450k Bob ENST00000355076 methyl5 9 ## 18 Methyl 450k Bob ENST00000383706 methyl5 10 longFormat(myMultiAssay[, , 1:2], colDataCols=\"age\") ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 7 sampleMap rows not in names(experiments) ## DataFrame with 18 rows and 6 columns ## assay primary rowname colname value age ## ## 1 Affy Jack ENST00000294241 array1 101 38 ## 2 Affy Jack ENST00000355076 array1 102 38 ## 3 Affy Jill ENST00000294241 array2 103 39 ## 4 Affy Jill ENST00000355076 array2 104 39 ## 5 Affy Barbara ENST00000294241 array3 105 41 ## ... ... ... ... ... ... ... ## 14 Methyl 450k Jill ENST00000383706 methyl3 6 39 ## 15 Methyl 450k Barbara ENST00000355076 methyl4 7 41 ## 16 Methyl 450k Barbara ENST00000383706 methyl4 8 41 ## 17 Methyl 450k Bob ENST00000355076 methyl5 9 40 ## 18 Methyl 450k Bob ENST00000383706 methyl5 10 40 maemerge <- mergeReplicates(intersectColumns(myMultiAssay)) ## harmonizing input: ## removing 1 sampleMap rows with 'colname' not in colnames of experiments wideFormat(maemerge, colDataCols=\"sex\")[, 1:5] ## DataFrame with 3 rows and 5 columns ## primary sex Affy_ENST00000294241 Affy_ENST00000355076 ## ## 1 Jack M 101 102 ## 2 Bob M 107 108 ## 3 Barbara F 105 106 ## Methyl.450k_ENST00000355076 ## ## 1 2 ## 2 9 ## 3 7"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"assay-assays","dir":"Articles","previous_headings":"Extractor functions","what":"assay / assays","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"assay (singular) function takes particular experiment returns matrix. default, return first experiment matrix. assays (plural) function returns SimpleList data matrices ExperimentList:","code":"assay(myMultiAssay) ## array1 array2 array3 array4 ## ENST00000294241 101 103 105 107 ## ENST00000355076 102 104 106 108 assays(myMultiAssay) ## List of length 4 ## names(4): Affy Methyl 450k Mirna CNV gistic"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"the-cancer-genome-atlas-and-multiassayexperiment","dir":"Articles","previous_headings":"","what":"The Cancer Genome Atlas and MultiAssayExperiment","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"recent efforts include release experiment data package, curatedTCGAData. package allow users selectively download cancer datasets Cancer Genome Atlas (TCGA) represent data MultiAssayExperiment objects. Please see package vignette details.","code":"BiocManager::install(\"curatedTCGAData\")"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"dimension-names-rownames-and-colnames","dir":"Articles","previous_headings":"","what":"Dimension names: rownames and colnames","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"rownames colnames return CharacterList row names column names across assays. CharacterList efficient alternative list used element contains character vector. also provides nice show method: back top","code":"rownames(myMultiAssay) ## CharacterList of length 4 ## [[\"Affy\"]] ENST00000294241 ENST00000355076 ## [[\"Methyl 450k\"]] ENST00000355076 ENST00000383706 ## [[\"Mirna\"]] hsa-miR-21 hsa-miR-191 hsa-miR-148a hsa-miR148b ## [[\"CNV gistic\"]] a b c d e colnames(myMultiAssay) ## CharacterList of length 4 ## [[\"Affy\"]] array1 array2 array3 array4 ## [[\"Methyl 450k\"]] methyl1 methyl2 methyl3 methyl4 methyl5 ## [[\"Mirna\"]] micro1 micro2 micro3 ## [[\"CNV gistic\"]] mysnparray1 mysnparray2 mysnparray3 mysnparray4"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"requirements-for-support-of-additional-data-classes","dir":"Articles","previous_headings":"","what":"Requirements for support of additional data classes","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"data classes ExperimentList object must support following methods: dimnames [ dim() happens one methods doesn’t:","code":"objlist2 <- objlist objlist2[[2]] <- as.vector(objlist2[[2]]) tryCatch( MultiAssayExperiment(objlist2, patient.data, dfmap), error = function(e) { conditionMessage(e) } ) ## [1] \"invalid class \\\"ExperimentList\\\" object: \\n 'integer' class is not supported, use a rectangular class\""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"application-programming-interface-api","dir":"Articles","previous_headings":"","what":"Application Programming Interface (API)","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"information formal API MultiAssayExperiment, please see API wiki document GitHub. API package available download GitHub via install(\"waldronlab/MultiAssayShiny\"). provides visual exploration available methods MultiAssayExperiment. back top","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"methods-for-multiassayexperiment","dir":"Articles","previous_headings":"","what":"Methods for MultiAssayExperiment","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"following methods defined MultiAssayExperiment:","code":"methods(class=\"MultiAssayExperiment\") ## [1] [ [[ [[<- [<- ## [5] $ $<- anyReplicated assay ## [9] assays c coerce colData ## [13] colData<- colnames<- complete.cases dimnames ## [17] drops drops<- experiments experiments<- ## [21] exportClass hasRowRanges isEmpty length ## [25] mergeReplicates metadata metadata<- names ## [29] names<- replicated replicates sampleMap ## [33] sampleMap<- show showReplicated splitAssays ## [37] subsetByAssay subsetByColData subsetByColumn subsetByRow ## [41] updateObject ## see '?methods' for accessing help and source code"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html","id":"sessioninfo","dir":"Articles","previous_headings":"","what":"sessionInfo()","title":"MultiAssayExperiment: The Integrative Bioconductor Container","text":"back top","code":"sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## ## Matrix products: default ## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 ## ## locale: ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C ## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 ## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 ## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C ## [9] LC_ADDRESS=C LC_TELEPHONE=C ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C ## ## time zone: Etc/UTC ## tzcode source: system (glibc) ## ## attached base packages: ## [1] stats4 stats graphics grDevices utils datasets methods ## [8] base ## ## other attached packages: ## [1] RaggedExperiment_1.28.1 MultiAssayExperiment_1.30.3 ## [3] SummarizedExperiment_1.34.0 Biobase_2.64.0 ## [5] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 ## [7] IRanges_2.38.1 S4Vectors_0.42.1 ## [9] BiocGenerics_0.50.0 MatrixGenerics_1.16.0 ## [11] matrixStats_1.3.0 BiocStyle_2.32.1 ## ## loaded via a namespace (and not attached): ## [1] xfun_0.46 bslib_0.8.0 htmlwidgets_1.6.4 ## [4] lattice_0.22-6 vctrs_0.6.5 tools_4.4.1 ## [7] generics_0.1.3 tibble_3.2.1 fansi_1.0.6 ## [10] highr_0.11 pkgconfig_2.0.3 BiocBaseUtils_1.6.0 ## [13] Matrix_1.7-0 desc_1.4.3 lifecycle_1.0.4 ## [16] GenomeInfoDbData_1.2.12 compiler_4.4.1 stringr_1.5.1 ## [19] textshaping_0.4.0 htmltools_0.5.8.1 sass_0.4.9 ## [22] yaml_2.3.10 pkgdown_2.1.0 pillar_1.9.0 ## [25] crayon_1.5.3 jquerylib_0.1.4 tidyr_1.3.1 ## [28] DelayedArray_0.30.1 cachem_1.1.0 abind_1.4-5 ## [31] tidyselect_1.2.1 digest_0.6.36 stringi_1.8.4 ## [34] purrr_1.0.2 dplyr_1.1.4 reshape2_1.4.4 ## [37] bookdown_0.40 fastmap_1.2.0 grid_4.4.1 ## [40] cli_3.6.3 SparseArray_1.4.8 magrittr_2.0.3 ## [43] S4Arrays_1.4.1 utf8_1.2.4 withr_3.0.1 ## [46] UCSC.utils_1.0.0 rmarkdown_2.27 XVector_0.44.0 ## [49] httr_1.4.7 ragg_1.3.2 evaluate_0.24.0 ## [52] knitr_1.48 rlang_1.1.4 Rcpp_1.0.13 ## [55] glue_1.7.0 BiocManager_1.30.23 jsonlite_1.8.8 ## [58] R6_2.5.1 plyr_1.8.9 systemfonts_1.1.0 ## [61] fs_1.6.4 zlibbioc_1.50.0"},{"path":[]},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"coldata---information-on-biological-units","dir":"Articles","previous_headings":"Component slots","what":"colData - information on biological units","title":"MultiAssayExperiment: Quick Start Guide","text":"DataFrame describing characteristics biological units, example clinical data patients. prepared datasets Cancer Genome Atlas, row one patient column clinical, pathological, subtype, variable. $ function provides shortcut accessing setting colData columns. Key points: * One row per patient * row maps zero observations experiment ExperimentList, .","code":"colData(miniACC)[1:4, 1:4] ## DataFrame with 4 rows and 4 columns ## patientID years_to_birth vital_status days_to_death ## ## TCGA-OR-A5J1 TCGA-OR-A5J1 58 1 1355 ## TCGA-OR-A5J2 TCGA-OR-A5J2 44 1 1677 ## TCGA-OR-A5J3 TCGA-OR-A5J3 23 0 NA ## TCGA-OR-A5J4 TCGA-OR-A5J4 23 1 423 table(miniACC$race) ## ## asian black or african american white ## 2 1 78"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"experimentlist---experiment-data","dir":"Articles","previous_headings":"Component slots","what":"ExperimentList - experiment data","title":"MultiAssayExperiment: Quick Start Guide","text":"base list ExperimentList object containing experimental datasets set samples collected. gets converted class ExperimentList construction. Key points: * One matrix-like dataset per list element (although even need matrix-like, see example RaggedExperiment package) * One matrix column per assayed specimen. matrix column must correspond exactly one row colData: words, must know patient cell line observation came . However, multiple columns can come patient, can data patient. * Matrix rows correspond variables, e.g. genes genomic ranges * ExperimentList elements can genomic range-based (e.g. SummarizedExperiment::RangedSummarizedExperiment-class RaggedExperiment::RaggedExperiment-class) ID-based data (e.g. SummarizedExperiment::SummarizedExperiment-class, Biobase::eSet-class base::matrix-class, DelayedArray::DelayedArray-class, derived classes) * data class can included ExperimentList, long supports: single-bracket subsetting ([), dimnames, dim. data classes defined Bioconductor meet requirements.","code":"experiments(miniACC) ## ExperimentList class object of length 5: ## [1] RNASeq2GeneNorm: SummarizedExperiment with 198 rows and 79 columns ## [2] gistict: SummarizedExperiment with 198 rows and 90 columns ## [3] RPPAArray: SummarizedExperiment with 33 rows and 46 columns ## [4] Mutations: matrix with 97 rows and 90 columns ## [5] miRNASeqGene: SummarizedExperiment with 471 rows and 80 columns"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"samplemap---relationship-graph","dir":"Articles","previous_headings":"Component slots","what":"sampleMap - relationship graph","title":"MultiAssayExperiment: Quick Start Guide","text":"sampleMap graph representation relationship biological units experimental results. simple cases column names ExperimentList data matrices match row names colData, user won’t need specify think sample map, can created automatically MultiAssayExperiment constructor. sampleMap simple three-column DataFrame: assay column: name assay, found names ExperimentList list names primary column: identifiers patients biological units, found row names colData colname column: identifiers assay results, found column names ExperimentList elements Helper functions available creating map list. See ?listToMap Key points: * relates experimental observations (colnames) colData * permits experiment-specific sample naming, missing, replicate observations back top","code":"sampleMap(miniACC) ## DataFrame with 385 rows and 3 columns ## assay primary colname ## ## 1 RNASeq2GeneNorm TCGA-OR-A5J1 TCGA-OR-A5J1-01A-11R.. ## 2 RNASeq2GeneNorm TCGA-OR-A5J2 TCGA-OR-A5J2-01A-11R.. ## 3 RNASeq2GeneNorm TCGA-OR-A5J3 TCGA-OR-A5J3-01A-11R.. ## 4 RNASeq2GeneNorm TCGA-OR-A5J5 TCGA-OR-A5J5-01A-11R.. ## 5 RNASeq2GeneNorm TCGA-OR-A5J6 TCGA-OR-A5J6-01A-31R.. ## ... ... ... ... ## 381 miRNASeqGene TCGA-PA-A5YG TCGA-PA-A5YG-01A-11R.. ## 382 miRNASeqGene TCGA-PK-A5H8 TCGA-PK-A5H8-01A-11R.. ## 383 miRNASeqGene TCGA-PK-A5H9 TCGA-PK-A5H9-01A-11R.. ## 384 miRNASeqGene TCGA-PK-A5HA TCGA-PK-A5HA-01A-11R.. ## 385 miRNASeqGene TCGA-PK-A5HB TCGA-PK-A5HB-01A-11R.."},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"metadata","dir":"Articles","previous_headings":"Component slots","what":"metadata","title":"MultiAssayExperiment: Quick Start Guide","text":"Metadata can used keep additional information patients, assays performed individuals entire cohort, features genes, proteins, genomic ranges. many options available storing metadata. First, MultiAssayExperiment metadata describing entire experiment: Additionally, DataFrame class used sampleMap colData, well ExperimentList class, similarly support metadata. Finally, many experimental data objects can used ExperimentList support metadata. provide flexible options users developers derived classes.","code":"metadata(miniACC) ## $title ## [1] \"Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma\" ## ## $PMID ## [1] \"27165744\" ## ## $sourceURL ## [1] \"http://s3.amazonaws.com/multiassayexperiments/accMAEO.rds\" ## ## $RPPAfeatureDataURL ## [1] \"http://genomeportal.stanford.edu/pan-tcga/show_target_selection_file?filename=Allprotein.txt\" ## ## $colDataExtrasURL ## [1] \"http://www.cell.com/cms/attachment/2062093088/2063584534/mmc3.xlsx\""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"single-bracket","dir":"Articles","previous_headings":"Subsetting","what":"Single bracket [","title":"MultiAssayExperiment: Quick Start Guide","text":"pseudo code , subsetting operations work rows following indices: 1. experimental data rows 2. j primary names column names (entered list List) 3. k assay Subsetting operations always return another MultiAssayExperiment. example, following return rows named “MAPK14” “IGFBP2”, remove assays rows match: following keep patients pathological stage iv, associated assays: following keep RNA-seq dataset, patients assay available:","code":"multiassayexperiment[i = rownames, j = primary or colnames, k = assay] miniACC[c(\"MAPK14\", \"IGFBP2\"), , ] stg4 <- miniACC$pathologic_stage == \"stage iv\" # remove NA values from vector miniACC[, stg4 & !is.na(stg4), ] miniACC[, , \"RNASeq2GeneNorm\"] ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 306 sampleMap rows not in names(experiments) ## removing 13 colData rownames not in sampleMap 'primary'"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"subsetting-by-genomic-ranges","dir":"Articles","previous_headings":"Subsetting > Single bracket [","what":"Subsetting by genomic ranges","title":"MultiAssayExperiment: Quick Start Guide","text":"ExperimentList objects features represented genomic ranges (e.g. RangedSummarizedExperiment, RaggedExperiment), GRanges object first subsetting position subset objects GenomicRanges::findOverlaps().","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"double-bracket","dir":"Articles","previous_headings":"Subsetting","what":"Double bracket [[","title":"MultiAssayExperiment: Quick Start Guide","text":"“double bracket” method ([[) convenience function extracting single element MultiAssayExperiment ExperimentList. avoids use experiments(mae)[[1L]]. example, following extract ExpressionSet object containing RNA-seq data:","code":"miniACC[[1L]] #or equivalently, miniACC[[\"RNASeq2GeneNorm\"]] ## class: SummarizedExperiment ## dim: 198 79 ## metadata(3): experimentData annotation protocolData ## assays(1): exprs ## rownames(198): DIRAS3 MAPK14 ... SQSTM1 KCNJ13 ## rowData names(0): ## colnames(79): TCGA-OR-A5J1-01A-11R-A29S-07 TCGA-OR-A5J2-01A-11R-A29S-07 ## ... TCGA-PK-A5HA-01A-11R-A29S-07 TCGA-PK-A5HB-01A-11R-A29S-07 ## colData names(0):"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"patients-with-complete-data","dir":"Articles","previous_headings":"Subsetting","what":"Patients with complete data","title":"MultiAssayExperiment: Quick Start Guide","text":"complete.cases() shows patients complete data assays: logical vector used patient subsetting. simply, intersectColumns() select complete cases rearrange ExperimentList element columns correspond exactly rows colData order: Note, column names assays accmatched assay-specific identifiers, automatically re-arranged correspond patients. TCGA assays, first three - delimited positions correspond patient, ie first patient TCGA--A5J2:","code":"summary(complete.cases(miniACC)) ## Mode FALSE TRUE ## logical 49 43 accmatched = intersectColumns(miniACC) colnames(accmatched) ## CharacterList of length 5 ## [[\"RNASeq2GeneNorm\"]] TCGA-OR-A5J2-01A-11R-A29S-07 ... ## [[\"gistict\"]] TCGA-OR-A5J2-01A-11D-A29H-01 ... TCGA-PK-A5HA-01A-11D-A29H-01 ## [[\"RPPAArray\"]] TCGA-OR-A5J2-01A-21-A39K-20 ... TCGA-PK-A5HA-01A-21-A39K-20 ## [[\"Mutations\"]] TCGA-OR-A5J2-01A-11D-A29I-10 ... TCGA-PK-A5HA-01A-11D-A29I-10 ## [[\"miRNASeqGene\"]] TCGA-OR-A5J2-01A-11R-A29W-13 ..."},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"row-names-that-are-common-across-assays","dir":"Articles","previous_headings":"Subsetting","what":"Row names that are common across assays","title":"MultiAssayExperiment: Quick Start Guide","text":"intersectRows() keeps rows common assay, aligns identical order. example, keep genes data available RNA-seq, GISTIC copy number, somatic mutations: back top","code":"accmatched2 <- intersectRows(miniACC[, , c(\"RNASeq2GeneNorm\", \"gistict\", \"Mutations\")]) ## Warning: 'experiments' dropped; see 'drops()' ## harmonizing input: ## removing 126 sampleMap rows not in names(experiments) rownames(accmatched2) ## CharacterList of length 3 ## [[\"RNASeq2GeneNorm\"]] DIRAS3 G6PD KDR ERBB3 AKT1S1 ... RET CDKN2A MACC1 CHGA ## [[\"gistict\"]] DIRAS3 G6PD KDR ERBB3 AKT1S1 ... PREX1 RET CDKN2A MACC1 CHGA ## [[\"Mutations\"]] DIRAS3 G6PD KDR ERBB3 AKT1S1 ... PREX1 RET CDKN2A MACC1 CHGA"},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"assay-and-assays","dir":"Articles","previous_headings":"Extraction","what":"assay and assays","title":"MultiAssayExperiment: Quick Start Guide","text":"assay assays methods follow SummarizedExperiment convention. assay (singular) method extract first element ExperimentList return matrix. assays (plural) method return SimpleList data element matrix. Key point: * Whereas [[ returned assay original class, assay() assays() convert assay data matrix form. back top","code":"class(assay(miniACC)) ## [1] \"matrix\" \"array\" assays(miniACC) ## List of length 5 ## names(5): RNASeq2GeneNorm gistict RPPAArray Mutations miRNASeqGene"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"summary-of-slots-and-accessors","dir":"Articles","previous_headings":"","what":"Summary of slots and accessors","title":"MultiAssayExperiment: Quick Start Guide","text":"Slot MultiAssayExperiment can accessed set using accessor functions: __*__ $ operator MultiAssayExperiment returns single column colData.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"transformation-reshaping","dir":"Articles","previous_headings":"","what":"Transformation / reshaping","title":"MultiAssayExperiment: Quick Start Guide","text":"longFormat wideFormat functions “reshape” combine experiments colData one DataFrame. functions provide compatibility common R/Bioconductor functions regression, machine learning, visualization.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"longformat","dir":"Articles","previous_headings":"Transformation / reshaping","what":"longFormat","title":"MultiAssayExperiment: Quick Start Guide","text":"long format single column provides assay results, additional optional colData columns whose values repeated necessary. assay name ExperimentList element, primary patient identifier (rowname colData), rowname assay rowname (case genes), colname assay-specific identifier (column name), value numeric measurement (gene expression, copy number, presence non-silent mutation, etc), following vital_status days_to_death colData columns added:","code":"longFormat(miniACC[c(\"TP53\", \"CTNNB1\"), , ], colDataCols = c(\"vital_status\", \"days_to_death\")) ## harmonizing input: ## removing 126 sampleMap rows not in names(experiments) ## DataFrame with 518 rows and 7 columns ## assay primary rowname colname ## ## 1 RNASeq2GeneNorm TCGA-OR-A5J1 TP53 TCGA-OR-A5J1-01A-11R-A29S-07 ## 2 RNASeq2GeneNorm TCGA-OR-A5J1 CTNNB1 TCGA-OR-A5J1-01A-11R-A29S-07 ## 3 RNASeq2GeneNorm TCGA-OR-A5J2 TP53 TCGA-OR-A5J2-01A-11R-A29S-07 ## 4 RNASeq2GeneNorm TCGA-OR-A5J2 CTNNB1 TCGA-OR-A5J2-01A-11R-A29S-07 ## 5 RNASeq2GeneNorm TCGA-OR-A5J3 TP53 TCGA-OR-A5J3-01A-11R-A29S-07 ## ... ... ... ... ... ## 514 Mutations TCGA-PK-A5HA CTNNB1 TCGA-PK-A5HA-01A-11D-A29I-10 ## 515 Mutations TCGA-PK-A5HB TP53 TCGA-PK-A5HB-01A-11D-A29I-10 ## 516 Mutations TCGA-PK-A5HB CTNNB1 TCGA-PK-A5HB-01A-11D-A29I-10 ## 517 Mutations TCGA-PK-A5HC TP53 TCGA-PK-A5HC-01A-11D-A30A-10 ## 518 Mutations TCGA-PK-A5HC CTNNB1 TCGA-PK-A5HC-01A-11D-A30A-10 ## value vital_status days_to_death ## ## 1 563.401 1 1355 ## 2 5634.467 1 1355 ## 3 165.481 1 1677 ## 4 62658.391 1 1677 ## 5 956.303 0 NA ## ... ... ... ... ## 514 0 0 NA ## 515 0 0 NA ## 516 0 0 NA ## 517 0 0 NA ## 518 0 0 NA"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"wideformat","dir":"Articles","previous_headings":"Transformation / reshaping","what":"wideFormat","title":"MultiAssayExperiment: Quick Start Guide","text":"wide format, feature assay goes separate column, one row per primary identifier (patient). , variable becomes new column:","code":"wideFormat(miniACC[c(\"TP53\", \"CTNNB1\"), , ], colDataCols = c(\"vital_status\", \"days_to_death\")) ## harmonizing input: ## removing 126 sampleMap rows not in names(experiments) ## DataFrame with 92 rows and 9 columns ## primary vital_status days_to_death RNASeq2GeneNorm_TP53 ## ## 1 TCGA-OR-A5J1 1 1355 563.401 ## 2 TCGA-OR-A5J2 1 1677 165.481 ## 3 TCGA-OR-A5J3 0 NA 956.303 ## 4 TCGA-OR-A5J4 1 423 NA ## 5 TCGA-OR-A5J5 1 365 1169.636 ## ... ... ... ... ... ## 88 TCGA-PK-A5H9 0 NA 890.866 ## 89 TCGA-PK-A5HA 0 NA 683.572 ## 90 TCGA-PK-A5HB 0 NA 237.370 ## 91 TCGA-PK-A5HC 0 NA NA ## 92 TCGA-P6-A5OG 1 383 815.345 ## RNASeq2GeneNorm_CTNNB1 gistict_TP53 gistict_CTNNB1 Mutations_TP53 ## ## 1 5634.47 0 0 0 ## 2 62658.39 0 1 1 ## 3 6337.43 0 0 0 ## 4 NA 1 0 0 ## 5 5979.06 0 0 0 ## ... ... ... ... ... ## 88 5258.99 0 0 0 ## 89 8120.17 -1 0 0 ## 90 5257.81 -1 -1 0 ## 91 NA 1 1 0 ## 92 6390.10 -1 1 NA ## Mutations_CTNNB1 ## ## 1 0 ## 2 1 ## 3 0 ## 4 0 ## 5 0 ## ... ... ## 88 0 ## 89 0 ## 90 0 ## 91 0 ## 92 NA"},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"multiassayexperiment-constructor-function","dir":"Articles","previous_headings":"MultiAssayExperiment class construction and concatenation","what":"MultiAssayExperiment constructor function","title":"MultiAssayExperiment: Quick Start Guide","text":"MultiAssayExperiment constructor function can take three arguments: experiments - ExperimentList list data colData - DataFrame describing patients (cell lines, biological units) sampleMap - DataFrame assay, primary, colname identifiers miniACC object can reconstructed follows:","code":"MultiAssayExperiment(experiments=experiments(miniACC), colData=colData(miniACC), sampleMap=sampleMap(miniACC), metadata=metadata(miniACC)) ## A MultiAssayExperiment object of 5 listed ## experiments with user-defined names and respective classes. ## Containing an ExperimentList class object of length 5: ## [1] RNASeq2GeneNorm: SummarizedExperiment with 198 rows and 79 columns ## [2] gistict: SummarizedExperiment with 198 rows and 90 columns ## [3] RPPAArray: SummarizedExperiment with 33 rows and 46 columns ## [4] Mutations: matrix with 97 rows and 90 columns ## [5] miRNASeqGene: SummarizedExperiment with 471 rows and 80 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"prepmultiassay---constructor-function-helper","dir":"Articles","previous_headings":"MultiAssayExperiment class construction and concatenation","what":"prepMultiAssay - Constructor function helper","title":"MultiAssayExperiment: Quick Start Guide","text":"prepMultiAssay function allows user diagnose typical problems creating MultiAssayExperiment object. See ?prepMultiAssay details.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"c---concatenate-to-multiassayexperiment","dir":"Articles","previous_headings":"MultiAssayExperiment class construction and concatenation","what":"c - concatenate to MultiAssayExperiment","title":"MultiAssayExperiment: Quick Start Guide","text":"c function allows user concatenate additional experiment existing MultiAssayExperiment. optional sampleMap argument allows concatenating assay whose column names match row names colData. convenience, mapFrom argument allows user map particular experiment provided order colnames . warning issued make user aware assumption. example, concatenate matrix log2-transformed RNA-seq results: back top","code":"miniACC2 <- c(miniACC, log2rnaseq = log2(assays(miniACC)$RNASeq2GeneNorm), mapFrom=1L) ## Warning: Assuming column order in the data provided ## matches the order in 'mapFrom' experiment(s) colnames assays(miniACC2) ## List of length 6 ## names(6): RNASeq2GeneNorm gistict RPPAArray Mutations miRNASeqGene log2rnaseq"},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"upsetr-venn-diagram","dir":"Articles","previous_headings":"Examples","what":"UpsetR “Venn” diagram","title":"MultiAssayExperiment: Quick Start Guide","text":"see 43 samples 5 assays, 32 missing reverse-phase protein (RPPAArray), 2 missing Mutations, 1 missing gistict, 12 mutations gistict, etc:","code":"library(UpSetR) upsetSamples(miniACC)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"kaplan-meier-plot-stratified-by-a-clinical-variable","dir":"Articles","previous_headings":"Examples","what":"Kaplan-meier plot stratified by a clinical variable","title":"MultiAssayExperiment: Quick Start Guide","text":"colData can provide clinical data things like Kaplan-Meier plot overall survival stratified nodal stage. simplify things, first add “y” column colData, containing Surv object survival analysis: Note: survfit method work well DataFrame. bypass error, covert colData data.frame. remove patients missing overall survival information:","code":"library(survival) library(survminer) coldat <- as.data.frame(colData(miniACC)) coldat$y <- Surv(miniACC$days_to_death, miniACC$vital_status) colData(miniACC) <- DataFrame(coldat) miniACC <- miniACC[, complete.cases(coldat$y), ] coldat <- as(colData(miniACC), \"data.frame\") fit <- survfit(y ~ pathology_N_stage, data = coldat) ggsurvplot(fit, data = coldat, risk.table = TRUE)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"multivariate-cox-regression-including-rna-seq-copy-number-and-pathology","dir":"Articles","previous_headings":"Examples","what":"Multivariate Cox regression including RNA-seq, copy number, and pathology","title":"MultiAssayExperiment: Quick Start Guide","text":"Choose EZH2 gene demonstration. subsetting drop assays row named EZH2: Perform multivariate Cox regression EZH2 copy number (gistict), log2-transformed EZH2 expression (RNASeq2GeneNorm), nodal status (pathology_N_stage) predictors: see EZH2 expression significantly associated overal survival (p < 0.001), EZH2 copy number nodal status . analysis easily extended whole genome discovery prognostic features repeated univariate regressions columns, penalized multivariate regression, etc. detail, see main MultiAssayExperiment vignette.","code":"wideacc <- wideFormat(miniACC[\"EZH2\", , ], colDataCols = c(\"vital_status\", \"days_to_death\", \"pathology_N_stage\")) ## harmonizing input: ## removing 76 sampleMap rows not in names(experiments) wideacc$y <- Surv(wideacc$days_to_death, wideacc$vital_status) head(wideacc) ## DataFrame with 6 rows and 7 columns ## primary vital_status days_to_death pathology_N_stage ## ## 1 TCGA-OR-A5J1 1 1355 n0 ## 2 TCGA-OR-A5J2 1 1677 n0 ## 3 TCGA-OR-A5J4 1 423 n1 ## 4 TCGA-OR-A5J5 1 365 n0 ## 5 TCGA-OR-A5J7 1 490 n0 ## 6 TCGA-OR-A5J8 1 579 n0 ## RNASeq2GeneNorm_EZH2 gistict_EZH2 y ## ## 1 75.8886 0 1355:1 ## 2 326.5332 1 1677:1 ## 3 NA -2 423:1 ## 4 366.3826 1 365:1 ## 5 747.6935 1 490:1 ## 6 426.4401 1 579:1 coxph(Surv(days_to_death, vital_status) ~ gistict_EZH2 + log2(RNASeq2GeneNorm_EZH2) + pathology_N_stage, data=wideacc) ## Call: ## coxph(formula = Surv(days_to_death, vital_status) ~ gistict_EZH2 + ## log2(RNASeq2GeneNorm_EZH2) + pathology_N_stage, data = wideacc) ## ## coef exp(coef) se(coef) z p ## gistict_EZH2 -0.03723 0.96345 0.28205 -0.132 0.894986 ## log2(RNASeq2GeneNorm_EZH2) 0.97731 2.65729 0.28105 3.477 0.000506 ## pathology_N_stagen1 0.37749 1.45862 0.56992 0.662 0.507743 ## ## Likelihood ratio test=16.28 on 3 df, p=0.0009942 ## n= 26, number of events= 26 ## (8 observations deleted due to missingness)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"MultiAssayExperiment: Quick Start Guide","text":"back top","code":"sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## ## Matrix products: default ## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 ## ## locale: ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C ## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 ## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 ## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C ## [9] LC_ADDRESS=C LC_TELEPHONE=C ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C ## ## time zone: Etc/UTC ## tzcode source: system (glibc) ## ## attached base packages: ## [1] stats4 stats graphics grDevices utils datasets methods ## [8] base ## ## other attached packages: ## [1] survminer_0.4.9 ggpubr_0.6.0 ## [3] ggplot2_3.5.1 survival_3.7-0 ## [5] UpSetR_1.4.0 MultiAssayExperiment_1.30.3 ## [7] SummarizedExperiment_1.34.0 Biobase_2.64.0 ## [9] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 ## [11] IRanges_2.38.1 S4Vectors_0.42.1 ## [13] BiocGenerics_0.50.0 MatrixGenerics_1.16.0 ## [15] matrixStats_1.3.0 BiocStyle_2.32.1 ## ## loaded via a namespace (and not attached): ## [1] tidyselect_1.2.1 dplyr_1.1.4 farver_2.1.2 ## [4] fastmap_1.2.0 digest_0.6.36 lifecycle_1.0.4 ## [7] magrittr_2.0.3 compiler_4.4.1 rlang_1.1.4 ## [10] sass_0.4.9 tools_4.4.1 utf8_1.2.4 ## [13] yaml_2.3.10 data.table_1.15.4 knitr_1.48 ## [16] ggsignif_0.6.4 S4Arrays_1.4.1 labeling_0.4.3 ## [19] htmlwidgets_1.6.4 DelayedArray_0.30.1 xml2_1.3.6 ## [22] plyr_1.8.9 abind_1.4-5 withr_3.0.1 ## [25] purrr_1.0.2 desc_1.4.3 grid_4.4.1 ## [28] fansi_1.0.6 xtable_1.8-4 colorspace_2.1-1 ## [31] scales_1.3.0 cli_3.6.3 rmarkdown_2.27 ## [34] crayon_1.5.3 ragg_1.3.2 generics_0.1.3 ## [37] km.ci_0.5-6 httr_1.4.7 reshape2_1.4.4 ## [40] commonmark_1.9.1 BiocBaseUtils_1.6.0 cachem_1.1.0 ## [43] stringr_1.5.1 zlibbioc_1.50.0 splines_4.4.1 ## [46] BiocManager_1.30.23 XVector_0.44.0 survMisc_0.5.6 ## [49] vctrs_0.6.5 Matrix_1.7-0 carData_3.0-5 ## [52] jsonlite_1.8.8 bookdown_0.40 car_3.1-2 ## [55] rstatix_0.7.2 systemfonts_1.1.0 tidyr_1.3.1 ## [58] jquerylib_0.1.4 glue_1.7.0 pkgdown_2.1.0 ## [61] ggtext_0.1.2 stringi_1.8.4 gtable_0.3.5 ## [64] UCSC.utils_1.0.0 munsell_0.5.1 tibble_3.2.1 ## [67] pillar_1.9.0 htmltools_0.5.8.1 GenomeInfoDbData_1.2.12 ## [70] KMsurv_0.1-5 R6_2.5.1 textshaping_0.4.0 ## [73] evaluate_0.24.0 lattice_0.22-6 markdown_1.13 ## [76] highr_0.11 backports_1.5.0 gridtext_0.1.5 ## [79] broom_1.0.6 bslib_0.8.0 Rcpp_1.0.13 ## [82] gridExtra_2.3 SparseArray_1.4.8 xfun_0.46 ## [85] zoo_1.8-12 fs_1.6.4 pkgconfig_2.0.3"},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/UsingHDF5Array.html","id":"dependencies","dir":"Articles","previous_headings":"Integrating an HDF5 backend for MultiAssayExperiment","what":"Dependencies","title":"Using DelayedMatrix with MultiAssayExperiment","text":"","code":"library(MultiAssayExperiment) library(HDF5Array) library(SummarizedExperiment)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/UsingHDF5Array.html","id":"hdf5array-and-delayedarray-constructor","dir":"Articles","previous_headings":"Integrating an HDF5 backend for MultiAssayExperiment","what":"HDF5Array and DelayedArray Constructor","title":"Using DelayedMatrix with MultiAssayExperiment","text":"HDF5Array package provides -disk representation large datasets without need load memory. Convenient lazy evaluation operations allow user manipulate large data files based metadata. DelayedMatrix class DelayedArray package provides way connect large matrix stored disk. First, create small matrix constructing DelayedMatrix class. add rownames column names matrix object compatibility MultiAssayExperiment representation. use DelayedArray constructor function create DelayedMatrix object.","code":"smallMatrix <- matrix(rnorm(10e5), ncol = 20) rownames(smallMatrix) <- paste0(\"GENE\", seq_len(nrow(smallMatrix))) colnames(smallMatrix) <- paste0(\"SampleID\", seq_len(ncol(smallMatrix))) smallMatrix <- DelayedArray(smallMatrix) class(smallMatrix) ## [1] \"DelayedMatrix\" ## attr(,\"package\") ## [1] \"DelayedArray\" # show method smallMatrix ## <50000 x 20> DelayedMatrix object of type \"double\": ## SampleID1 SampleID2 SampleID3 ... SampleID19 SampleID20 ## GENE1 -1.400043517 1.431663588 -1.336606503 . -2.307774531 -2.293199815 ## GENE2 0.255317055 0.171127984 0.089914742 . 0.614199996 -0.335822358 ## GENE3 -2.437263611 2.312015552 0.379995935 . -0.733181166 0.083092829 ## GENE4 -0.005571287 -0.057850207 -0.056034294 . 0.818604632 0.106635015 ## GENE5 0.621552721 -0.975709562 0.700863028 . 0.005259257 1.643080357 ## ... . . . . . . ## GENE49996 0.2027090 0.4424774 0.6336781 . -0.47392601 0.28854415 ## GENE49997 1.2847634 1.2558989 1.2587418 . -2.52268507 -1.77342923 ## GENE49998 0.2648680 1.3883708 -0.3003243 . -1.76756368 0.76883529 ## GENE49999 1.4098422 0.2065422 -0.4955832 . 1.59338432 -0.05131006 ## GENE50000 -0.7546331 0.6750468 0.1188484 . -1.25230132 0.30771323 dim(smallMatrix) ## [1] 50000 20"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/UsingHDF5Array.html","id":"writing-to-a-file-with-dimnames","dir":"Articles","previous_headings":"Integrating an HDF5 backend for MultiAssayExperiment","what":"Writing to a file with dimnames","title":"Using DelayedMatrix with MultiAssayExperiment","text":"Finally, rhdf5 package stores dimnames standard location. order make use functionality, use writeHDF5Array .dimnames argument: see file structure use h5ls:","code":"testh5 <- tempfile(fileext = \".h5\") writeHDF5Array(smallMatrix, filepath = testh5, name = \"smallMatrix\", with.dimnames = TRUE) ## <50000 x 20> HDF5Matrix object of type \"double\": ## SampleID1 SampleID2 SampleID3 ... SampleID19 SampleID20 ## GENE1 -1.400043517 1.431663588 -1.336606503 . -2.307774531 -2.293199815 ## GENE2 0.255317055 0.171127984 0.089914742 . 0.614199996 -0.335822358 ## GENE3 -2.437263611 2.312015552 0.379995935 . -0.733181166 0.083092829 ## GENE4 -0.005571287 -0.057850207 -0.056034294 . 0.818604632 0.106635015 ## GENE5 0.621552721 -0.975709562 0.700863028 . 0.005259257 1.643080357 ## ... . . . . . . ## GENE49996 0.2027090 0.4424774 0.6336781 . -0.47392601 0.28854415 ## GENE49997 1.2847634 1.2558989 1.2587418 . -2.52268507 -1.77342923 ## GENE49998 0.2648680 1.3883708 -0.3003243 . -1.76756368 0.76883529 ## GENE49999 1.4098422 0.2065422 -0.4955832 . 1.59338432 -0.05131006 ## GENE50000 -0.7546331 0.6750468 0.1188484 . -1.25230132 0.30771323 h5ls(testh5) ## group name otype dclass dim ## 0 / .smallMatrix_dimnames H5I_GROUP ## 1 /.smallMatrix_dimnames 1 H5I_DATASET STRING 50000 ## 2 /.smallMatrix_dimnames 2 H5I_DATASET STRING 20 ## 3 / smallMatrix H5I_DATASET FLOAT 50000 x 20"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/UsingHDF5Array.html","id":"importing-hdf5-files","dir":"Articles","previous_headings":"Integrating an HDF5 backend for MultiAssayExperiment","what":"Importing HDF5 files","title":"Using DelayedMatrix with MultiAssayExperiment","text":"Note large matrix HDF5 file can also loaded using HDF5ArraySeed DelayedArray functions.","code":"hdf5Data <- HDF5ArraySeed(file = testh5, name = \"smallMatrix\") newDelayedMatrix <- DelayedArray(hdf5Data) class(newDelayedMatrix) ## [1] \"HDF5Matrix\" ## attr(,\"package\") ## [1] \"HDF5Array\" newDelayedMatrix ## <50000 x 20> HDF5Matrix object of type \"double\": ## SampleID1 SampleID2 SampleID3 ... SampleID19 SampleID20 ## GENE1 -1.400043517 1.431663588 -1.336606503 . -2.307774531 -2.293199815 ## GENE2 0.255317055 0.171127984 0.089914742 . 0.614199996 -0.335822358 ## GENE3 -2.437263611 2.312015552 0.379995935 . -0.733181166 0.083092829 ## GENE4 -0.005571287 -0.057850207 -0.056034294 . 0.818604632 0.106635015 ## GENE5 0.621552721 -0.975709562 0.700863028 . 0.005259257 1.643080357 ## ... . . . . . . ## GENE49996 0.2027090 0.4424774 0.6336781 . -0.47392601 0.28854415 ## GENE49997 1.2847634 1.2558989 1.2587418 . -2.52268507 -1.77342923 ## GENE49998 0.2648680 1.3883708 -0.3003243 . -1.76756368 0.76883529 ## GENE49999 1.4098422 0.2065422 -0.4955832 . 1.59338432 -0.05131006 ## GENE50000 -0.7546331 0.6750468 0.1188484 . -1.25230132 0.30771323"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/UsingHDF5Array.html","id":"using-a-delayedmatrix-with-multiassayexperiment","dir":"Articles","previous_headings":"Integrating an HDF5 backend for MultiAssayExperiment","what":"Using a DelayedMatrix with MultiAssayExperiment","title":"Using DelayedMatrix with MultiAssayExperiment","text":"DelayedMatrix alone conforms MultiAssayExperiment API requirements. Shown , DelayedMatrix can put named list passed MultiAssayExperiment constructor function.","code":"HDF5MAE <- MultiAssayExperiment(experiments = list(smallMatrix = smallMatrix)) sampleMap(HDF5MAE) ## DataFrame with 20 rows and 3 columns ## assay primary colname ## ## 1 smallMatrix SampleID1 SampleID1 ## 2 smallMatrix SampleID2 SampleID2 ## 3 smallMatrix SampleID3 SampleID3 ## 4 smallMatrix SampleID4 SampleID4 ## 5 smallMatrix SampleID5 SampleID5 ## ... ... ... ... ## 16 smallMatrix SampleID16 SampleID16 ## 17 smallMatrix SampleID17 SampleID17 ## 18 smallMatrix SampleID18 SampleID18 ## 19 smallMatrix SampleID19 SampleID19 ## 20 smallMatrix SampleID20 SampleID20 colData(HDF5MAE) ## DataFrame with 20 rows and 0 columns"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/UsingHDF5Array.html","id":"summarizedexperiment-with-delayedmatrix-backend","dir":"Articles","previous_headings":"Integrating an HDF5 backend for MultiAssayExperiment > Using a DelayedMatrix with MultiAssayExperiment","what":"SummarizedExperiment with DelayedMatrix backend","title":"Using DelayedMatrix with MultiAssayExperiment","text":"information rich DelayedMatrix can created used conjunction SummarizedExperiment class can even include rowRanges. flexibility MultiAssayExperiment API supports classes minimal requirements. Additionally, SummarizedExperiment DelayedMatrix backend can part bigger MultiAssayExperiment object. minimal example work: Additional scenarios currently development HDF5Matrix hosted remotely. Many opportunities exist considering -disk -disk representations data MultiAssayExperiment.","code":"HDF5SE <- SummarizedExperiment(assays = smallMatrix) assay(HDF5SE) ## <50000 x 20> DelayedMatrix object of type \"double\": ## SampleID1 SampleID2 SampleID3 ... SampleID19 SampleID20 ## GENE1 -1.400043517 1.431663588 -1.336606503 . -2.307774531 -2.293199815 ## GENE2 0.255317055 0.171127984 0.089914742 . 0.614199996 -0.335822358 ## GENE3 -2.437263611 2.312015552 0.379995935 . -0.733181166 0.083092829 ## GENE4 -0.005571287 -0.057850207 -0.056034294 . 0.818604632 0.106635015 ## GENE5 0.621552721 -0.975709562 0.700863028 . 0.005259257 1.643080357 ## ... . . . . . . ## GENE49996 0.2027090 0.4424774 0.6336781 . -0.47392601 0.28854415 ## GENE49997 1.2847634 1.2558989 1.2587418 . -2.52268507 -1.77342923 ## GENE49998 0.2648680 1.3883708 -0.3003243 . -1.76756368 0.76883529 ## GENE49999 1.4098422 0.2065422 -0.4955832 . 1.59338432 -0.05131006 ## GENE50000 -0.7546331 0.6750468 0.1188484 . -1.25230132 0.30771323 MultiAssayExperiment(list(HDF5SE = HDF5SE)) ## A MultiAssayExperiment object of 1 listed ## experiment with a user-defined name and respective class. ## Containing an ExperimentList class object of length 1: ## [1] HDF5SE: SummarizedExperiment with 50000 rows and 20 columns ## Functionality: ## experiments() - obtain the ExperimentList instance ## colData() - the primary/phenotype DataFrame ## sampleMap() - the sample coordination DataFrame ## `$`, `[`, `[[` - extract colData columns, subset, or experiment ## *Format() - convert into a long or wide DataFrame ## assays() - convert ExperimentList to a SimpleList of matrices ## exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/UsingHDF5Array.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"Using DelayedMatrix with MultiAssayExperiment","text":"","code":"sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## ## Matrix products: default ## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 ## ## locale: ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C ## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 ## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 ## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C ## [9] LC_ADDRESS=C LC_TELEPHONE=C ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C ## ## time zone: Etc/UTC ## tzcode source: system (glibc) ## ## attached base packages: ## [1] stats4 stats graphics grDevices utils datasets methods ## [8] base ## ## other attached packages: ## [1] HDF5Array_1.32.1 rhdf5_2.48.0 ## [3] DelayedArray_0.30.1 SparseArray_1.4.8 ## [5] S4Arrays_1.4.1 abind_1.4-5 ## [7] Matrix_1.7-0 MultiAssayExperiment_1.30.3 ## [9] SummarizedExperiment_1.34.0 Biobase_2.64.0 ## [11] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 ## [13] IRanges_2.38.1 S4Vectors_0.42.1 ## [15] BiocGenerics_0.50.0 MatrixGenerics_1.16.0 ## [17] matrixStats_1.3.0 BiocStyle_2.32.1 ## ## loaded via a namespace (and not attached): ## [1] sass_0.4.9 lattice_0.22-6 digest_0.6.36 ## [4] evaluate_0.24.0 grid_4.4.1 bookdown_0.40 ## [7] fastmap_1.2.0 jsonlite_1.8.8 BiocManager_1.30.23 ## [10] httr_1.4.7 UCSC.utils_1.0.0 textshaping_0.4.0 ## [13] jquerylib_0.1.4 cli_3.6.3 rlang_1.1.4 ## [16] crayon_1.5.3 XVector_0.44.0 cachem_1.1.0 ## [19] yaml_2.3.10 tools_4.4.1 Rhdf5lib_1.26.0 ## [22] GenomeInfoDbData_1.2.12 R6_2.5.1 lifecycle_1.0.4 ## [25] zlibbioc_1.50.0 fs_1.6.4 htmlwidgets_1.6.4 ## [28] ragg_1.3.2 desc_1.4.3 pkgdown_2.1.0 ## [31] bslib_0.8.0 systemfonts_1.1.0 xfun_0.46 ## [34] knitr_1.48 rhdf5filters_1.16.0 htmltools_0.5.8.1 ## [37] rmarkdown_2.27 compiler_4.4.1"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/extras/MAE-curatedMetagenomicData.html","id":"fetch-from-curatedmetagenomicdata","dir":"Articles > Extras","previous_headings":"","what":"Fetch from curatedMetagenomicData","title":"Making use of curatedMetagenomicData","text":"Download data ExpressionSet list: Create MultiAssayExperiment:","code":"library(curatedMetagenomicData) esetlist <- list(taxa = ZellerG_2014.metaphlan_bugs_list.stool()[, 1:10], pathways = ZellerG_2014.pathabundance_relab.stool()) ## species and strain-level taxa only: esetlist$taxa <- esetlist$taxa[grep(\"s__\", rownames(esetlist$taxa)), ] ## eliminate taxa-specific pathway contributions (only total pathway abundances): esetlist$pathways <- esetlist$pathways[grep(\"g__\", rownames(esetlist$pathways), invert=TRUE), ] library(MultiAssayExperiment) cmd <- MultiAssayExperiment(experiments=esetlist, colData=colData(as(esetlist[[2]], \"SummarizedExperiment\"))) cmd rownames(cmd)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/extras/MAE-curatedMetagenomicData.html","id":"cca-with-omicade4","dir":"Articles > Extras","previous_headings":"Fetch from curatedMetagenomicData","what":"CCA with omicade4","title":"Making use of curatedMetagenomicData","text":"","code":"library(omicade4) cmdsub <- cmd[, cmd$disease %in% c(\"adenoma\", \"CRC\", \"healthy\"), ] ##Get rid of rows that are all zero: cmdsub <- cmdsub[lapply(assays(cmdsub), function(exper) rowSums(exper) > 0), ] mcoin <- mcia(assay(cmdsub)) plot(mcoin, phenovec=cmdsub$disease, sample.lab=FALSE)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/extras/MAE-curatedMetagenomicData.html","id":"iclusterplus","dir":"Articles > Extras","previous_headings":"Fetch from curatedMetagenomicData","what":"iClusterPlus","title":"Making use of curatedMetagenomicData","text":"Error, “system computationally singular”","code":"library(iClusterPlus) datasets = assay(cmdsub) datasets = lapply(datasets, t) iclus = iCluster(datasets=datasets, k=5, lambda=c(0.2, 0.2)) plotiCluster(fit=iclus, label=cmdsub$disease)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/extras/MAE-curatedMetagenomicData.html","id":"sparse-cca","dir":"Articles > Extras","previous_headings":"Fetch from curatedMetagenomicData","what":"sparse CCA","title":"Making use of curatedMetagenomicData","text":"","code":"library(PMA) cmd2 <- mergeReplicates(intersectColumns(cmd)) ## ERROR: some columns have SD = 0 mycca <- PMA::CCA(x=t(assay(cmd2, 1)), z=t(assay(cmd2, 2))) mycca"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/articles/extras/MAE-curatedMetagenomicData.html","id":"others-to-try","dir":"Articles > Extras","previous_headings":"","what":"Others to try","title":"Making use of curatedMetagenomicData","text":"","code":"library(made4) library(MCIA) # library(Rtopper) # gene set analysis"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Marcel Ramos. Author, maintainer. Martin Morgan. Author, contributor. Lori Shepherd. Contributor. Hervé Pagès. Contributor. Vincent J Carey. Author, contributor. Levi Waldron. Author. MultiAssay SIG. Contributor.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ramos M, Schiffer L, Re , Azhar R, Basunia , Rodriguez Cabrera C, Chan T, Chapman P, Davis S, Gomez-Cabrero D, Culhane , Haibe-Kains B, Hansen K, Kodali H, Louis M, Mer , Reister M, Morgan M, Carey V, Waldron L (2017). “Software Integration Multi-Omics Experiments Bioconductor.” Cancer Research, 77(21), e39-42. doi:10.1158/0008-5472.CAN-17-0344, https://cancerres.aacrjournals.org/content/77/21/e39.","code":"@Article{, title = {Software For The Integration Of Multi-Omics Experiments In Bioconductor}, author = {Marcel Ramos and Lucas Schiffer and Angela Re and Rimsha Azhar and Azfar Basunia and Carmen {Rodriguez Cabrera} and Tiffany Chan and Philip Chapman and Sean Davis and David Gomez-Cabrero and Aedin C. Culhane and Benjamin Haibe-Kains and Kasper Hansen and Hanish Kodali and Marie S Louis and Arvind S Mer and Markus Reister and Martin Morgan and Vincent J Carey and Levi Waldron}, journal = {Cancer Research}, year = {2017}, volume = {77}, number = {21}, pages = {e39-42}, doi = {10.1158/0008-5472.CAN-17-0344}, url = {https://cancerres.aacrjournals.org/content/77/21/e39}, }"},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/index.html","id":"software-for-the-integration-of-multi-omics-experiments-in-bioconductor","dir":"","previous_headings":"","what":"Software For The Integration Of Multi-Omics Experiments In Bioconductor","title":"Software for the integration of multi-omics experiments in Bioconductor","text":"https://doi.org/10.1158/0008-5472.CAN-17-0344","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Software for the integration of multi-omics experiments in Bioconductor","text":"recommend installing stable release version MultiAssayExperiment Bioconductor. can done using BiocManager:","code":"if (!require(\"BiocManager\")) install.packages(\"BiocManager\") library(BiocManager) install(\"MultiAssayExperiment\")"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/index.html","id":"schematic","dir":"","previous_headings":"","what":"Schematic","title":"Software for the integration of multi-omics experiments in Bioconductor","text":"visual overview MultiAssayExperiment class. three main components : colData - phenotype data ExperimentList - list tables experimental results sampleMap - graph representation ‘samples’ ‘participants’ Note. simplicity, use terms ‘samples’ ‘participants’ elucidate relationship although MultiAssayExperiment can work biological specimens.","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/index.html","id":"ready-to-use-multiassayexperiment-objects","dir":"","previous_headings":"","what":"Ready-to-use MultiAssayExperiment objects","title":"Software for the integration of multi-omics experiments in Bioconductor","text":"easy--use ready-made MultiAssayExperiment objects, use curatedTCGAData experiment data package.","code":"install(\"curatedTCGAData\")"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/index.html","id":"companion-package-for-working-with-tcga-data","dir":"","previous_headings":"","what":"Companion package for working with TCGA data","title":"Software for the integration of multi-omics experiments in Bioconductor","text":"TCGAutils handy package working MultiAssayExperiment data objects curatedTCGAData. highly recommended use TCGAutils identifier manipulation, sample identification .","code":"install(\"TCGAutils\")"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"Software for the integration of multi-omics experiments in Bioconductor","text":"MultiAssayExperiment API available browsing API wiki.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/index.html","id":"the-multiassayexperiment-bioconductor-special-interest-group","dir":"","previous_headings":"","what":"The MultiAssayExperiment Bioconductor Special Interest Group","title":"Software for the integration of multi-omics experiments in Bioconductor","text":"group meets remotely discuss project approximately every 3 weeks. interested, please join MultiAssayExperiment Google Group see calendar upcoming meetings.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/index.html","id":"contributor-code-of-conduct","dir":"","previous_headings":"","what":"Contributor Code of Conduct","title":"Software for the integration of multi-omics experiments in Bioconductor","text":"contributors maintainers project, pledge respect people contribute reporting issues, posting feature requests, updating documentation, submitting pull requests patches, activities. committed making participation project harassment-free experience everyone, regardless level experience, gender, gender identity expression, sexual orientation, disability, personal appearance, body size, race, age, religion. Examples unacceptable behavior participants include use sexual language imagery, derogatory comments personal attacks, trolling, public private harassment, insults, disrespectful conduct. Project maintainers right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct. Project maintainers follow Code Conduct may removed project team. Instances abusive, harassing, otherwise unacceptable behavior may reported opening issue contacting one project maintainers. Code Conduct adapted Contributor Covenant, version 1.0.0, available http://contributor-covenant.org/version/1/0/0/","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList-class.html","id":null,"dir":"Reference","previous_headings":"","what":"ExperimentList - A container for multi-experiment data — ExperimentList-class","title":"ExperimentList - A container for multi-experiment data — ExperimentList-class","text":"ExperimentList class container builds SimpleList additional checks consistency experiment names length. contains SimpleList experiments sample identifiers. One element present per experiment performed. Convert SimpleList list multi-experiment data container. using mergeReplicates method, additional arguments passed given simplify function argument (e.g., na.rm = TRUE)","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ExperimentList - A container for multi-experiment data — ExperimentList-class","text":"","code":"# S4 method for class 'ExperimentList' show(object) # S4 method for class 'ExperimentList' isEmpty(x) # S4 method for class 'ExperimentList' dimnames(x) # S4 method for class 'ExperimentList' colnames(x, do.NULL = TRUE, prefix = \"col\") # S4 method for class 'ExperimentList' rownames(x, do.NULL = TRUE, prefix = \"row\") # S4 method for class 'ExperimentList' mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...) # S4 method for class 'ANY,missing' assay(x, i, withDimnames = TRUE, ...) # S4 method for class 'ExperimentList' assays(x, withDimnames = TRUE, ...) # S4 method for class 'ExperimentList,missing' assay(x, i, withDimnames = TRUE, ...) # S4 method for class 'ExperimentList,numeric' assay(x, i, withDimnames = TRUE, ...) # S4 method for class 'ExperimentList,character' assay(x, i, withDimnames = TRUE, ...)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ExperimentList - A container for multi-experiment data — ExperimentList-class","text":"object, x ExperimentList object .NULL, prefix See ?base::rownames description arguments. replicates mergeReplicates: list LogicalList element represents sample vector repeated measurements sample simplify function merging columns duplicates indicated replicates ... Additional arguments. See details information. scalar character integer index withDimnames logical (default TRUE) whether return dimension names","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ExperimentList - A container for multi-experiment data — ExperimentList-class","text":"ExperimentList class object","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"ExperimentList - A container for multi-experiment data — ExperimentList-class","text":"show(ExperimentList): Show method ExperimentList class isEmpty(ExperimentList): check zero length across experiments dimnames(ExperimentList): Get dimension names ExperimentList using CharacterList colnames(ExperimentList): Get column names ExperimentList CharacterList slightly efficiently rownames(ExperimentList): Get row names ExperimentList CharacterList slightly efficiently mergeReplicates(ExperimentList): Apply mergeReplicates method ExperimentList elements assay(x = , = missing): Obtain specified assay numeric character reference assays(ExperimentList): Get assay data element ExperimentList","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList-class.html","id":"coercion","dir":"Reference","previous_headings":"","what":"coercion","title":"ExperimentList - A container for multi-experiment data — ExperimentList-class","text":"Convert list S4 List ExperimentList using () function. following example, x either list List:","code":"as(x, \"ExperimentList\")"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ExperimentList - A container for multi-experiment data — ExperimentList-class","text":"","code":"ExperimentList() #> ExperimentList class object of length 0: #>"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList.html","id":null,"dir":"Reference","previous_headings":"","what":"Represent multiple experiments as a List-derivative ExperimentList — ExperimentList","title":"Represent multiple experiments as a List-derivative ExperimentList — ExperimentList","text":"ExperimentList class can contain several different types data. requirements ExperimentList class objects contained following set methods: dim, [, dimnames","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Represent multiple experiments as a List-derivative ExperimentList — ExperimentList","text":"","code":"ExperimentList(...)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Represent multiple experiments as a List-derivative ExperimentList — ExperimentList","text":"... named list class object","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Represent multiple experiments as a List-derivative ExperimentList — ExperimentList","text":"ExperimentList class object experiment data","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Represent multiple experiments as a List-derivative ExperimentList — ExperimentList","text":"","code":"## Create an empty ExperimentList instance ExperimentList() #> ExperimentList class object of length 0: #> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, dimnames = list( c(\"ENST00000294241\", \"ENST00000355076\", \"ENST00000383706\",\"ENST00000234812\", \"ENST00000383323\"), c(\"array1\", \"array2\", \"array3\", \"array4\") )) colDat <- data.frame(slope53 = rnorm(4), row.names = c(\"array1\", \"array2\", \"array3\", \"array4\")) ## SummarizedExperiment constructor exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, colData = colDat) ## Create a sample methylation dataset methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, dimnames = list( c(\"ENST00000355076\", \"ENST00000383706\", \"ENST00000383323\", \"ENST00000234812\", \"ENST00000294241\"), c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\") )) ## Create a sample RNASeqGene dataset rnadat <- matrix( data = sample(c(46851, 5, 19, 13, 2197, 507, 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), ncol = 4, dimnames = list( c(\"XIST\", \"RPS4Y1\", \"KDM5D\", \"ENST00000383323\", \"ENST00000234812\"), c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\") )) ## Create a mock RangedSummarizedExperiment from a data.frame rangedat <- data.frame(chr=\"chr2\", start = 11:15, end = 12:16, strand = c(\"+\", \"-\", \"+\", \"*\", \".\"), samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), row.names = c(paste0(\"ENST\", \"00000\", 135411:135414), \"ENST00000383323\")) rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) ## Combine to a named list and call the ExperimentList constructor function assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, GISTIC = rangeSE) ## Use the ExperimentList constructor ExpList <- ExperimentList(assayList)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/HDF5MultiAssayExperiment.html","id":null,"dir":"Reference","previous_headings":"","what":"Save a MultiAssayExperiment class object to HDF5 and Rds files — saveHDF5MultiAssayExperiment","title":"Save a MultiAssayExperiment class object to HDF5 and Rds files — saveHDF5MultiAssayExperiment","text":"function takes MultiAssayExperiment object uses assays functionality obtain data matrices experiments. saved .h5 file format. function relies heavily HDF5Array package whose installation required use. saveHDF5MultiAssayExpeirment preserves classes contained ExperimentList exception matrix converted HDF5Matrix. Internal SummarizedExperiment assays converted HDF5-backed assays HDF5Array::saveHDF5SummarizedExperiment. SummarizedExperiment objects multiple -th assays first assay take precedence others assays dropped warning. first assay SummarizedExperiment contains array, array preserved process saving loading HDF5-backed MultiAssayExperiment.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/HDF5MultiAssayExperiment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Save a MultiAssayExperiment class object to HDF5 and Rds files — saveHDF5MultiAssayExperiment","text":"","code":"saveHDF5MultiAssayExperiment( x, dir = \"h5_mae\", prefix = NULL, replace = FALSE, chunkdim = NULL, level = NULL, as.sparse = NA, verbose = NA ) loadHDF5MultiAssayExperiment(dir = \"h5_mae\", prefix = NULL)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/HDF5MultiAssayExperiment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Save a MultiAssayExperiment class object to HDF5 and Rds files — saveHDF5MultiAssayExperiment","text":"x MultiAssayExperiment object derivative dir path (single string) directory save HDF5-based MultiAssayExperiment object load . saving, directory created already exist. directory already exists prefix specified replace set TRUE, replaced empty directory. prefix optional prefix add names files created inside dir. allows saving one object directory. prefix NULL, name x input MultiAssayExperiment used. avoid default setting use empty character string .e., \"\". underscore (_) appended prefix provided; therefore, typical inputs words, e.g., \"test\". replace prefix specified, pre-existing directory replaced new empty one? content pre-existing directory lost! chunkdim, level dimensions chunks compression level use writing assay data disk. Passed internal calls writeHDF5Array. See ?writeHDF5Array information. .sparse Whether assay data flagged sparse . set NA (default), specific .sparse value use assay determined calling is_sparse() . Passed internal calls writeHDF5Array. See ?writeHDF5Array information IMPORTANT NOTE. verbose Set TRUE make function display progress. case saveHDF5MultiAssayExperiment(), verbose set NA default, case verbosity controlled DelayedArray.verbose.block.processing option. Setting verbose TRUE FALSE overrides option.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/HDF5MultiAssayExperiment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Save a MultiAssayExperiment class object to HDF5 and Rds files — saveHDF5MultiAssayExperiment","text":"","code":"data(\"miniACC\") testDir <- file.path(tempdir(), \"test_mae\") saveHDF5MultiAssayExperiment( miniACC, dir = testDir, verbose = TRUE, replace = TRUE ) #> Start writing assay 1/5 to HDF5 file: #> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> / reading and realizing block 1/1 ... #> ok #> \\ Writing it ... #> OK #> Finished writing assay 1/5 to HDF5 file: #> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> Start writing assay 2/5 to HDF5 file: #> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> / reading and realizing block 1/1 ... #> ok #> \\ Writing it ... #> OK #> Finished writing assay 2/5 to HDF5 file: #> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> Start writing assay 3/5 to HDF5 file: #> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> / reading and realizing block 1/1 ... #> ok #> \\ Writing it ... #> OK #> Finished writing assay 3/5 to HDF5 file: #> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> Start writing assay 4/5 to HDF5 file: #> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> / reading and realizing block 1/1 ... #> ok #> \\ Writing it ... #> OK #> Finished writing assay 4/5 to HDF5 file: #> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> Start writing assay 5/5 to HDF5 file: #> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> / reading and realizing block 1/1 ... #> ok #> \\ Writing it ... #> OK #> Finished writing assay 5/5 to HDF5 file: #> /tmp/RtmpRerB1M/test_mae/miniACC_experiments.h5 #> Serialize MultiAssayExperiment object to RDS file: #> /tmp/RtmpRerB1M/test_mae/miniACC_mae.rds ## inspect the files in the dir list.files(testDir) #> [1] \"miniACC_experiments.h5\" \"miniACC_mae.rds\" loadHDF5MultiAssayExperiment( dir = testDir ) #> A MultiAssayExperiment object of 5 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 5: #> [1] RNASeq2GeneNorm: SummarizedExperiment with 198 rows and 79 columns #> [2] gistict: SummarizedExperiment with 198 rows and 90 columns #> [3] RPPAArray: SummarizedExperiment with 33 rows and 46 columns #> [4] Mutations: HDF5Matrix with 97 rows and 90 columns #> [5] miRNASeqGene: SummarizedExperiment with 471 rows and 80 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## remove example files unlink(testDir, recursive = TRUE)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MatchedAssayExperiment-class.html","id":null,"dir":"Reference","previous_headings":"","what":"MatchedAssayExperiment - A matched-samples MultiAssayExperiment class — MatchedAssayExperiment-class","title":"MatchedAssayExperiment - A matched-samples MultiAssayExperiment class — MatchedAssayExperiment-class","text":"class supports use matched samples equal number observations per biological unit present assays.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MatchedAssayExperiment-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MatchedAssayExperiment - A matched-samples MultiAssayExperiment class — MatchedAssayExperiment-class","text":"","code":"MatchedAssayExperiment(...)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MatchedAssayExperiment-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MatchedAssayExperiment - A matched-samples MultiAssayExperiment class — MatchedAssayExperiment-class","text":"... Either single MultiAssayExperiment components create valid MultiAssayExperiment","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MatchedAssayExperiment-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MatchedAssayExperiment - A matched-samples MultiAssayExperiment class — MatchedAssayExperiment-class","text":"MatchedAssayExperiment object","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MatchedAssayExperiment-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"MatchedAssayExperiment - A matched-samples MultiAssayExperiment class — MatchedAssayExperiment-class","text":"MatchedAssayExperiment(): Construct MatchedAssayExperiment class MultiAssayExperiment","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MatchedAssayExperiment-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"MatchedAssayExperiment - A matched-samples MultiAssayExperiment class — MatchedAssayExperiment-class","text":"","code":"data(\"miniACC\") acc <- as(miniACC, \"MatchedAssayExperiment\") acc #> A MatchedAssayExperiment object of 5 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 5: #> [1] RNASeq2GeneNorm: SummarizedExperiment with 198 rows and 43 columns #> [2] gistict: SummarizedExperiment with 198 rows and 43 columns #> [3] RPPAArray: SummarizedExperiment with 33 rows and 43 columns #> [4] Mutations: matrix with 97 rows and 43 columns #> [5] miRNASeqGene: SummarizedExperiment with 471 rows and 43 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":null,"dir":"Reference","previous_headings":"","what":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"MultiAssayExperiment class can used manage results diverse assays collection specimen. Currently, class can handle assays organized instances SummarizedExperiment, ExpressionSet, matrix, RaggedExperiment (inherits GRangesList), RangedVcfStack. Create new MultiAssayExperiment instances homonymous constructor, minimally argument ExperimentList, potentially also arguments colData (see section ) sampleMap.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"","code":"# S4 method for class 'MultiAssayExperiment' show(object) # S4 method for class 'MultiAssayExperiment' length(x) # S4 method for class 'MultiAssayExperiment' names(x) # S4 method for class 'MultiAssayExperiment' updateObject(object, ..., verbose = FALSE) # S4 method for class 'MultiAssayExperiment' dimnames(x) # S4 method for class 'MultiAssayExperiment' c(x, ..., sampleMap = NULL, mapFrom = NULL) # S4 method for class 'MultiAssayExperiment' exportClass( object, dir = tempdir(), fmt, ext, match = FALSE, verbose = TRUE, ... ) # S4 method for class 'MultiAssayExperiment' assays(x, withDimnames = TRUE, ...) # S4 method for class 'MultiAssayExperiment,missing' assay(x, i, withDimnames = TRUE, ...) # S4 method for class 'MultiAssayExperiment,numeric' assay(x, i, withDimnames = TRUE, ...) # S4 method for class 'MultiAssayExperiment,character' assay(x, i, withDimnames = TRUE, ...)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"object, x MultiAssayExperiment object ... Additional arguments supporting functions. See details. verbose logical(1) Whether print additional information (default TRUE) sampleMap c method: sampleMap list DataFrame guide merge mapFrom Either logical, character, integer vector indicating experiment(s) identical colname order experiment input(s). using character input, name must match exactly. dir character(1) directory saving exported data (default: tempdir()) fmt character(1) function() Either format character atomic supported write.table either ('csv', 'tsv') function whose first two arguments 'object save' 'file location' ext character(1) file extension supported format argument match logical(1) Whether coerce current object 'MatchedAssayExperiment' object (default: FALSE) withDimnames logical (default TRUE) whether return dimension names included object integer character scalar indicating assay return","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"MultiAssayExperiment object","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"dots (...) argument allows user specify additional arguments several instances. subsetting [: additional arguments sent findOverlaps. mergeReplicates: used specify arguments simplify functional argument assay: may contain withDimnames, forwarded assays combining c: compatible MultiAssayExperiment classes passed ExperimentList constructor, can list, List, series named arguments. See examples .","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"show(MultiAssayExperiment): Show method MultiAssayExperiment length(MultiAssayExperiment): Get length ExperimentList names(MultiAssayExperiment): Get names ExperimentList updateObject(MultiAssayExperiment): Update old serialized MultiAssayExperiment objects new API dimnames(MultiAssayExperiment): Get dimension names MultiAssayExperiment object c(MultiAssayExperiment): Add supported data class ExperimentList exportClass(MultiAssayExperiment): Export data class series text files assays(MultiAssayExperiment): Obtain SimpleList assay data available experiments object assay(x = MultiAssayExperiment, = missing): Convenience function extracting assay first element (default) ExperimentList. numeric character index can also provided","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"ExperimentList ExperimentList class object assay dataset colData DataFrame clinical/specimen data available across experiments sampleMap DataFrame translatable identifiers samples participants metadata Additional data describing MultiAssayExperiment object drops metadata list dropped information","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"coldata","dir":"Reference","previous_headings":"","what":"colData","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"colData slot collection primary specimen data valid across experiments. slot strictly class DataFrame arguments constructor function allow arguments class data.frame subsequently coerced.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"experimentlist","dir":"Reference","previous_headings":"","what":"ExperimentList","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"ExperimentList slot designed contain results experiment/assay. contains SimpleList.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"samplemap","dir":"Reference","previous_headings":"","what":"sampleMap","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"sampleMap contains DataFrame translatable identifiers samples participants biological units. standard column names sampleMap \"assay\", \"primary\", \"colname\". Note \"assay\" column factor corresponding names experiment ExperimentList. case names match sampleMap experiments, documented experiments sampleMap take precedence experiments dropped harmonization procedure. constructor function generate sampleMap case provided method may 'safer' alternative creating MultiAssayExperiment (long rownames identical colData, provided). empty sampleMap may produce empty experiments levels \"assay\" factor sampleMap match names ExperimentList.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"coercion","dir":"Reference","previous_headings":"","what":"coercion","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"Convert list S4 List MultiAssayExperiment object using methods::function. following example, x either list List: (x, \"MultiAssayExperiment\") Convert MultiAssayExperiment MAF class object using methods::function. following example, x MultiAssayExperiment: MultiAssayExperimentToMAF(x)","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"MultiAssayExperiment - An integrative multi-assay class for experiment data — MultiAssayExperiment-class","text":"","code":"example(\"MultiAssayExperiment\") #> #> MltAsE> ## Run the example ExperimentList #> MltAsE> example(\"ExperimentList\") #> #> ExprmL> ## Create an empty ExperimentList instance #> ExprmL> ExperimentList() #> ExperimentList class object of length 0: #> #> ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class #> ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000294241\", \"ENST00000355076\", #> ExprmL+ \"ENST00000383706\",\"ENST00000234812\", \"ENST00000383323\"), #> ExprmL+ c(\"array1\", \"array2\", \"array3\", \"array4\") #> ExprmL+ )) #> #> ExprmL> colDat <- data.frame(slope53 = rnorm(4), #> ExprmL+ row.names = c(\"array1\", \"array2\", \"array3\", \"array4\")) #> #> ExprmL> ## SummarizedExperiment constructor #> ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, #> ExprmL+ colData = colDat) #> #> ExprmL> ## Create a sample methylation dataset #> ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000355076\", \"ENST00000383706\", #> ExprmL+ \"ENST00000383323\", \"ENST00000234812\", \"ENST00000294241\"), #> ExprmL+ c(\"methyl1\", \"methyl2\", \"methyl3\", #> ExprmL+ \"methyl4\", \"methyl5\") #> ExprmL+ )) #> #> ExprmL> ## Create a sample RNASeqGene dataset #> ExprmL> rnadat <- matrix( #> ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507, #> ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), #> ExprmL+ ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"XIST\", \"RPS4Y1\", \"KDM5D\", \"ENST00000383323\", \"ENST00000234812\"), #> ExprmL+ c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\") #> ExprmL+ )) #> #> ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame #> ExprmL> rangedat <- data.frame(chr=\"chr2\", start = 11:15, end = 12:16, #> ExprmL+ strand = c(\"+\", \"-\", \"+\", \"*\", \".\"), #> ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), #> ExprmL+ row.names = c(paste0(\"ENST\", \"00000\", 135411:135414), \"ENST00000383323\")) #> #> ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) #> #> ExprmL> ## Combine to a named list and call the ExperimentList constructor function #> ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, #> ExprmL+ GISTIC = rangeSE) #> #> ExprmL> ## Use the ExperimentList constructor #> ExprmL> ExpList <- ExperimentList(assayList) #> #> MltAsE> ## Create sample maps for each experiment #> MltAsE> exprmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"array1\", \"array2\", \"array3\", \"array4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> methylmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> rnamap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\"), #> MltAsE+ colname = c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> gistmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Bob\", \"Jill\"), #> MltAsE+ colname = c(\"samp0\", \"samp1\", \"samp2\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> ## Combine as a named list and convert to a DataFrame #> MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap, #> MltAsE+ RNASeqGene = rnamap, GISTIC = gistmap) #> #> MltAsE> ## Create a sampleMap #> MltAsE> sampMap <- listToMap(maplist) #> #> MltAsE> ## Create an example phenotype data #> MltAsE> colDat <- data.frame(sex = c(\"M\", \"F\", \"M\", \"F\"), age = 38:41, #> MltAsE+ row.names = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\")) #> #> MltAsE> ## Create a MultiAssayExperiment instance #> MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat, #> MltAsE+ sampleMap = sampMap) ## Subsetting # Rows (i) Rows/Features in each experiment mae[1, , ] #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 1 rows and 4 columns #> [2] Methyl450k: matrix with 1 rows and 5 columns #> [3] RNASeqGene: matrix with 1 rows and 4 columns #> [4] GISTIC: RangedSummarizedExperiment with 1 rows and 3 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files mae[c(TRUE, FALSE), , ] #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 3 rows and 4 columns #> [2] Methyl450k: matrix with 3 rows and 5 columns #> [3] RNASeqGene: matrix with 3 rows and 4 columns #> [4] GISTIC: RangedSummarizedExperiment with 3 rows and 3 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files # Columns (j) Rows in colData mae[, rownames(colData(mae))[3:2], ] #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 5 rows and 2 columns #> [2] Methyl450k: matrix with 5 rows and 2 columns #> [3] RNASeqGene: matrix with 5 rows and 2 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 2 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files # Assays (k) mae[, , \"Affy\"] #> Warning: 'experiments' dropped; see 'drops()' #> harmonizing input: #> removing 12 sampleMap rows not in names(experiments) #> A MultiAssayExperiment object of 1 listed #> experiment with a user-defined name and respective class. #> Containing an ExperimentList class object of length 1: #> [1] Affy: SummarizedExperiment with 5 rows and 4 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Complete cases (returns logical vector) completes <- complete.cases(mae) compMAE <- mae[, completes, ] compMAE #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 5 rows and 3 columns #> [2] Methyl450k: matrix with 5 rows and 4 columns #> [3] RNASeqGene: matrix with 5 rows and 3 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 3 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files colData(compMAE) #> DataFrame with 3 rows and 2 columns #> sex age #> #> Jack M 38 #> Jill F 39 #> Bob M 40 example(\"MultiAssayExperiment\") #> #> MltAsE> ## Run the example ExperimentList #> MltAsE> example(\"ExperimentList\") #> #> ExprmL> ## Create an empty ExperimentList instance #> ExprmL> ExperimentList() #> ExperimentList class object of length 0: #> #> ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class #> ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000294241\", \"ENST00000355076\", #> ExprmL+ \"ENST00000383706\",\"ENST00000234812\", \"ENST00000383323\"), #> ExprmL+ c(\"array1\", \"array2\", \"array3\", \"array4\") #> ExprmL+ )) #> #> ExprmL> colDat <- data.frame(slope53 = rnorm(4), #> ExprmL+ row.names = c(\"array1\", \"array2\", \"array3\", \"array4\")) #> #> ExprmL> ## SummarizedExperiment constructor #> ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, #> ExprmL+ colData = colDat) #> #> ExprmL> ## Create a sample methylation dataset #> ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000355076\", \"ENST00000383706\", #> ExprmL+ \"ENST00000383323\", \"ENST00000234812\", \"ENST00000294241\"), #> ExprmL+ c(\"methyl1\", \"methyl2\", \"methyl3\", #> ExprmL+ \"methyl4\", \"methyl5\") #> ExprmL+ )) #> #> ExprmL> ## Create a sample RNASeqGene dataset #> ExprmL> rnadat <- matrix( #> ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507, #> ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), #> ExprmL+ ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"XIST\", \"RPS4Y1\", \"KDM5D\", \"ENST00000383323\", \"ENST00000234812\"), #> ExprmL+ c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\") #> ExprmL+ )) #> #> ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame #> ExprmL> rangedat <- data.frame(chr=\"chr2\", start = 11:15, end = 12:16, #> ExprmL+ strand = c(\"+\", \"-\", \"+\", \"*\", \".\"), #> ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), #> ExprmL+ row.names = c(paste0(\"ENST\", \"00000\", 135411:135414), \"ENST00000383323\")) #> #> ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) #> #> ExprmL> ## Combine to a named list and call the ExperimentList constructor function #> ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, #> ExprmL+ GISTIC = rangeSE) #> #> ExprmL> ## Use the ExperimentList constructor #> ExprmL> ExpList <- ExperimentList(assayList) #> #> MltAsE> ## Create sample maps for each experiment #> MltAsE> exprmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"array1\", \"array2\", \"array3\", \"array4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> methylmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> rnamap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\"), #> MltAsE+ colname = c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> gistmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Bob\", \"Jill\"), #> MltAsE+ colname = c(\"samp0\", \"samp1\", \"samp2\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> ## Combine as a named list and convert to a DataFrame #> MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap, #> MltAsE+ RNASeqGene = rnamap, GISTIC = gistmap) #> #> MltAsE> ## Create a sampleMap #> MltAsE> sampMap <- listToMap(maplist) #> #> MltAsE> ## Create an example phenotype data #> MltAsE> colDat <- data.frame(sex = c(\"M\", \"F\", \"M\", \"F\"), age = 38:41, #> MltAsE+ row.names = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\")) #> #> MltAsE> ## Create a MultiAssayExperiment instance #> MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat, #> MltAsE+ sampleMap = sampMap) ## Add an experiment test1 <- mae[[1L]] colnames(test1) <- rownames(colData(mae)) ## Combine current MultiAssayExperiment with additional experiment ## (no sampleMap) c(mae, newExperiment = test1) #> A MultiAssayExperiment object of 5 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 5: #> [1] Affy: SummarizedExperiment with 5 rows and 4 columns #> [2] Methyl450k: matrix with 5 rows and 5 columns #> [3] RNASeqGene: matrix with 5 rows and 4 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 3 columns #> [5] newExperiment: SummarizedExperiment with 5 rows and 4 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files test2 <- mae[[3L]] c(mae, newExp = test2, mapFrom = 3L) #> Warning: Assuming column order in the data provided #> matches the order in 'mapFrom' experiment(s) colnames #> A MultiAssayExperiment object of 5 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 5: #> [1] Affy: SummarizedExperiment with 5 rows and 4 columns #> [2] Methyl450k: matrix with 5 rows and 5 columns #> [3] RNASeqGene: matrix with 5 rows and 4 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 3 columns #> [5] newExp: matrix with 5 rows and 4 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Add experiment using experiment name in mapFrom c(mae, RNASeqGeneV2 = test2, mapFrom = \"RNASeqGene\") #> Warning: Assuming column order in the data provided #> matches the order in 'mapFrom' experiment(s) colnames #> A MultiAssayExperiment object of 5 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 5: #> [1] Affy: SummarizedExperiment with 5 rows and 4 columns #> [2] Methyl450k: matrix with 5 rows and 5 columns #> [3] RNASeqGene: matrix with 5 rows and 4 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 3 columns #> [5] RNASeqGeneV2: matrix with 5 rows and 4 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":null,"dir":"Reference","previous_headings":"","what":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"set helper functions created help clean manipulate MultiAssayExperiment object. intersectRows also works ExperimentList objects. complete.cases: Returns logical vector corresponding 'colData' rows data across experiments isEmpty: Returns logical TRUE value zero length MultiAssayExperiment objects intersectRows: Takes common rows across experiments, excludes experiments empty rownames intersectColumns: wrapper complete.cases return MultiAssayExperiment biological units measurements across experiments replicated: Identifies, via logical vectors, colnames originate single biological unit within assay replicates: Provides replicate colnames found replicated function name, empty list none anyReplicated: Whether assay replicate measurements showReplicated: Displays actual columns replicated per assay biological unit, .e., primary value (colData rowname) sampleMap mergeReplicates: function combines replicated / repeated measurements across experiments guided replicated return value longFormat: MultiAssayExperiment method returns small skinny DataFrame. colDataCols arguments allows user append colData columns data. wideFormat: function reshape data MultiAssayExperiment \"wide\" format DataFrame. row DataFrame represents observation (corresponding entry colData). replicates present, data appended end corresponding row generate additional NA data. recommended remove consolidate technical replicates mergeReplicates. Optional colDataCols can added original object MultiAssayExperiment. hasRowRanges: function identifies ExperimentList elements rowRanges method getWithColData: convenience function extracting assay associated colData renamePrimary: convenience function rename primary biological units represented rownames(colData) renameColname: convenience function rename colnames particular assay","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"","code":"# S4 method for class 'MultiAssayExperiment' complete.cases(...) # S4 method for class 'MultiAssayExperiment' isEmpty(x) intersectRows(x) intersectColumns(x) replicated(x) # S4 method for class 'MultiAssayExperiment' replicated(x) anyReplicated(x) # S4 method for class 'MultiAssayExperiment' anyReplicated(x) showReplicated(x) # S4 method for class 'MultiAssayExperiment' showReplicated(x) replicates(x, ...) # S4 method for class 'MultiAssayExperiment' replicates(x, ...) mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...) # S4 method for class 'MultiAssayExperiment' mergeReplicates( x, replicates = replicated(x), simplify = BiocGenerics::mean, ... ) # S4 method for class 'ANY' mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...) longFormat(object, colDataCols = NULL, i = 1L) wideFormat( object, colDataCols = NULL, check.names = TRUE, collapse = \"_\", i = 1L ) hasRowRanges(x) # S4 method for class 'MultiAssayExperiment' hasRowRanges(x) # S4 method for class 'ExperimentList' hasRowRanges(x) getWithColData(x, i, mode = c(\"append\", \"replace\"), verbose = FALSE) renamePrimary(x, value) renameColname(x, i, value) splitAssays(x, hitList) # S4 method for class 'MultiAssayExperiment' splitAssays(x, hitList) makeHitList(x, patternList)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"... Additional arguments. See details information. x MultiAssayExperiment ExperimentList replicates list LogicalLists indicating multiple / duplicate entries biological unit per assay, see replicated (default replicated(x)). simplify function merging repeat measurements experiments indicated replicated method MultiAssayExperiment object supported class object colDataCols character, logical, numeric index colData columns included longFormat: -th assay SummarizedExperiment-like objects. vector input supported case SummarizedExperiment object(s) one assay (default 1L), renameColname: Either numeric character index indicating assay whose colnames renamed check.names (logical default TRUE) Column names output DataFrame checked syntactic validity made unique, necessary collapse (character default \"_\") single string delimiter output column names. wideFormat, experiments rownames (replicate samples present, colnames) seperated delimiter mode String indicating MultiAssayExperiment column-level metadata added SummarizedExperiment colData. verbose logical(1) Whether suppressMessages subsetting operations getWithColData (default FALSE) value renamePrimary: character vector length existing rownames(colData) use replacement, renameColname: CharacterList list matching lengths replace colnames(x) hitList named list List logical vectors indicate groupings assays patternList named list List atomic character vectors input grepl identifying groupings assays","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"See itemized list description section details.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"replicated function finds replicate measurements assay returns list LogicalLists. element single LogicalList corresponds biological primary unit sampleMap. small graphic one particular biological unit one assay, logical vector corresponds number measurements/samples assay: anyReplicated determines assays least one replicate. Note. methods available ExperimentList class due missing sampleMap structure (design). showReplicated returns list CharacterLists element corresponds biological primary units replicated assay element. values inner list colnames assay technical replicates. replicates function (noun) returns colnames sampleMap identified replicates. returns list CharacterLists assay present MultiAssayExperiment inner entry biological unit replicate observations assay. mergeReplicates function house-keeping method MultiAssayExperiment complete.cases returned. -assay operation averages replicate measurements (default) columns aligned row order colData. Users can provide function merging replicates simplify functional argument. Additional inputs ... sent 'simplify' function. mergeReplicates \"\" method consolidates duplicate measurements rectangular data structures, returns object class (endomorphic). ellipsis ... argument allows user provide additional arguments simplify functional argument. longFormat \"\" class method, works classes ExpressionSet SummarizedExperiment well matrix provide consistent long skinny DataFrame. hasRowRanges method identifies assays support rowRanges method return GRanges object.","code":"> replicated(MultiAssayExperiment) (list str) '-- $ AssayName (LogicalList str) '-- [[ \"Biological Unit\" ]] Replicated if sum(...) > 1 '-- TRUE TRUE FALSE FALSE"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"mergereplicates","dir":"Reference","previous_headings":"","what":"mergeReplicates","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"mergeReplicates function makes use output replicated point duplicate measurements biological unit MultiAssayExperiment. function return MultiAssayExperiment merged replicates. Additional arguments can provided simplify argument via ellipsis (...). example, replicates \"TCGA-B\" \"TCGA-\" found assay, name first appearing replicate taken (.e., \"B\"). Note typical use case merging replicates occurs multiple measurements sample (within assay) can therefore averaged.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"longformat","dir":"Reference","previous_headings":"","what":"longFormat","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"'longFormat' method takes data ExperimentList MultiAssayExperiment returns uniform DataFrame. resulting DataFrame columns indicating primary, rowname, colname value. method can optionally include columns MultiAssayExperiment colData named colDataCols character vector argument. (MultiAssayExperiment method ). argument allows user specify assay value SummarizedExperiment assay function's argument.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"wideformat","dir":"Reference","previous_headings":"","what":"wideFormat","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"wideFormat function returns standardized wide DataFrame row represents biological unit colData. Depending data setup, biological units can patients, tumors, specimens, etc. Metadata columns generated based names produced wide format DataFrame. can accessed via mcols() function. See wideFormat section description colDataCols arguments.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"hasrowranges","dir":"Reference","previous_headings":"","what":"hasRowRanges","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"hasRowRanges method identifies assays associated ranged row data directly testing method object. result test must GRanges class object satisfy test.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"getwithcoldata","dir":"Reference","previous_headings":"","what":"getWithColData","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"getWithColData function allows user conveniently extract particular assay indicated index argument. also attempt provide colData along extracted object using colData<- replacement method possible. Typically, method available SummarizedExperiment RaggedExperiment classes. setting mode determines colData added. mode=\"append\", MultiAssayExperiment metadata appended onto SummarizedExperiment. fields duplicated name, values SummarizedExperiment retained, warning emitted values different. mode=\"replace\", MultiAssayExperiment metadata replaces SummarizedExperiment, mode=\"none\", replacement appending performed.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"rename-","dir":"Reference","previous_headings":"","what":"rename*","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"renamePrimary function allows user conveniently change actual names primary biological units seen rownames(colData). renameColname allows user change names particular assay based index . can either single numeric character value. See colnames<- method renaming multiple colnames MultiAssayExperiment.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"splitassays","dir":"Reference","previous_headings":"","what":"splitAssays","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"splitAssays method separates columns assays based hitList input. hitList can generated using makeHitList helper function. use makeHitList helper, user input list patterns match column names assay. matches mutually exclusive avoid repetition columns across assays. See examples section.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A group of helper functions for manipulating and cleaning a MultiAssayExperiment — MultiAssayExperiment-helpers","text":"","code":"example(MultiAssayExperiment) #> #> MltAsE> ## Run the example ExperimentList #> MltAsE> example(\"ExperimentList\") #> #> ExprmL> ## Create an empty ExperimentList instance #> ExprmL> ExperimentList() #> ExperimentList class object of length 0: #> #> ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class #> ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000294241\", \"ENST00000355076\", #> ExprmL+ \"ENST00000383706\",\"ENST00000234812\", \"ENST00000383323\"), #> ExprmL+ c(\"array1\", \"array2\", \"array3\", \"array4\") #> ExprmL+ )) #> #> ExprmL> colDat <- data.frame(slope53 = rnorm(4), #> ExprmL+ row.names = c(\"array1\", \"array2\", \"array3\", \"array4\")) #> #> ExprmL> ## SummarizedExperiment constructor #> ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, #> ExprmL+ colData = colDat) #> #> ExprmL> ## Create a sample methylation dataset #> ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000355076\", \"ENST00000383706\", #> ExprmL+ \"ENST00000383323\", \"ENST00000234812\", \"ENST00000294241\"), #> ExprmL+ c(\"methyl1\", \"methyl2\", \"methyl3\", #> ExprmL+ \"methyl4\", \"methyl5\") #> ExprmL+ )) #> #> ExprmL> ## Create a sample RNASeqGene dataset #> ExprmL> rnadat <- matrix( #> ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507, #> ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), #> ExprmL+ ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"XIST\", \"RPS4Y1\", \"KDM5D\", \"ENST00000383323\", \"ENST00000234812\"), #> ExprmL+ c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\") #> ExprmL+ )) #> #> ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame #> ExprmL> rangedat <- data.frame(chr=\"chr2\", start = 11:15, end = 12:16, #> ExprmL+ strand = c(\"+\", \"-\", \"+\", \"*\", \".\"), #> ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), #> ExprmL+ row.names = c(paste0(\"ENST\", \"00000\", 135411:135414), \"ENST00000383323\")) #> #> ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) #> #> ExprmL> ## Combine to a named list and call the ExperimentList constructor function #> ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, #> ExprmL+ GISTIC = rangeSE) #> #> ExprmL> ## Use the ExperimentList constructor #> ExprmL> ExpList <- ExperimentList(assayList) #> #> MltAsE> ## Create sample maps for each experiment #> MltAsE> exprmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"array1\", \"array2\", \"array3\", \"array4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> methylmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> rnamap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\"), #> MltAsE+ colname = c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> gistmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Bob\", \"Jill\"), #> MltAsE+ colname = c(\"samp0\", \"samp1\", \"samp2\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> ## Combine as a named list and convert to a DataFrame #> MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap, #> MltAsE+ RNASeqGene = rnamap, GISTIC = gistmap) #> #> MltAsE> ## Create a sampleMap #> MltAsE> sampMap <- listToMap(maplist) #> #> MltAsE> ## Create an example phenotype data #> MltAsE> colDat <- data.frame(sex = c(\"M\", \"F\", \"M\", \"F\"), age = 38:41, #> MltAsE+ row.names = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\")) #> #> MltAsE> ## Create a MultiAssayExperiment instance #> MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat, #> MltAsE+ sampleMap = sampMap) complete.cases(mae) #> [1] TRUE TRUE TRUE FALSE isEmpty(MultiAssayExperiment()) #> [1] TRUE ## renaming biological units (primary) mae2 <- renamePrimary(mae, paste0(\"pt\", 1:4)) colData(mae2) #> DataFrame with 4 rows and 2 columns #> sex age #> #> pt1 M 38 #> pt2 F 39 #> pt3 M 40 #> pt4 F 41 sampleMap(mae2) #> DataFrame with 16 rows and 3 columns #> assay primary colname #> #> 1 Affy pt1 array1 #> 2 Affy pt2 array2 #> 3 Affy pt4 array3 #> 4 Affy pt3 array4 #> 5 Methyl450k pt1 methyl1 #> ... ... ... ... #> 12 RNASeqGene pt3 samparray3 #> 13 RNASeqGene pt4 samparray4 #> 14 GISTIC pt1 samp0 #> 15 GISTIC pt3 samp1 #> 16 GISTIC pt2 samp2 ## renaming observational units (colname) mae2 <- renameColname(mae, i = \"Affy\", paste0(\"ARRAY\", 1:4)) colnames(mae2) #> CharacterList of length 4 #> [[\"Affy\"]] ARRAY1 ARRAY2 ARRAY3 ARRAY4 #> [[\"Methyl450k\"]] methyl1 methyl2 methyl3 methyl4 methyl5 #> [[\"RNASeqGene\"]] samparray1 samparray2 samparray3 samparray4 #> [[\"GISTIC\"]] samp0 samp1 samp2 sampleMap(mae2) #> DataFrame with 16 rows and 3 columns #> assay primary colname #> #> 1 Affy Jack ARRAY1 #> 2 Affy Jill ARRAY2 #> 3 Affy Barbara ARRAY3 #> 4 Affy Bob ARRAY4 #> 5 Methyl450k Jack methyl1 #> ... ... ... ... #> 12 RNASeqGene Bob samparray3 #> 13 RNASeqGene Barbara samparray4 #> 14 GISTIC Jack samp0 #> 15 GISTIC Bob samp1 #> 16 GISTIC Jill samp2 patts <- list( normals = \"TCGA-[A-Z0-9]{2}-[A-Z0-9]{4}-11\", tumors = \"TCGA-[A-Z0-9]{2}-[A-Z0-9]{4}-01\" ) data(\"miniACC\") hits <- makeHitList(miniACC, patts) ## only turmors present splitAssays(miniACC, hits) #> A MultiAssayExperiment object of 5 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 5: #> [1] tumors_RNASeq2GeneNorm: SummarizedExperiment with 198 rows and 79 columns #> [2] tumors_gistict: SummarizedExperiment with 198 rows and 90 columns #> [3] tumors_RPPAArray: SummarizedExperiment with 33 rows and 46 columns #> [4] tumors_Mutations: matrix with 97 rows and 90 columns #> [5] tumors_miRNASeqGene: SummarizedExperiment with 471 rows and 80 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Accessing and modifying information in MultiAssayExperiment — MultiAssayExperiment-methods","title":"Accessing and modifying information in MultiAssayExperiment — MultiAssayExperiment-methods","text":"set accessor setter generic functions extract either sampleMap, ExperimentList, colData, metadata slots MultiAssayExperiment object","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Accessing and modifying information in MultiAssayExperiment — MultiAssayExperiment-methods","text":"","code":"# S4 method for class 'MultiAssayExperiment' sampleMap(x) # S4 method for class 'MultiAssayExperiment' experiments(x) # S4 method for class 'MultiAssayExperiment' colData(x, ...) # S4 method for class 'MultiAssayExperiment' drops(x) # S4 method for class 'MultiAssayExperiment,DataFrame' sampleMap(object) <- value # S4 method for class 'MultiAssayExperiment,ANY' sampleMap(object) <- value drops(x, ...) <- value # S4 method for class 'MultiAssayExperiment,ExperimentList' experiments(object) <- value # S4 method for class 'MultiAssayExperiment,List' experiments(object) <- value # S4 method for class 'MultiAssayExperiment,DataFrame' colData(x) <- value # S4 method for class 'MultiAssayExperiment,ANY' colData(x) <- value # S4 method for class 'MultiAssayExperiment' drops(x, ...) <- value # S4 method for class 'MultiAssayExperiment' x$name <- value # S4 method for class 'MultiAssayExperiment' names(x) <- value # S4 method for class 'MultiAssayExperiment,List' colnames(x) <- value # S4 method for class 'MultiAssayExperiment,list' colnames(x) <- value # S4 method for class 'MultiAssayExperiment' x$name # S4 method for class 'MultiAssayExperiment' metadata(x, ...) # S4 method for class 'MultiAssayExperiment' metadata(x, ...) <- value"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Accessing and modifying information in MultiAssayExperiment — MultiAssayExperiment-methods","text":"... Argument use object, x MultiAssayExperiment object value See details. name column colData","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Accessing and modifying information in MultiAssayExperiment — MultiAssayExperiment-methods","text":"Accessors: Either sampleMap, ExperimentList, DataFrame object Setters: MultiAssayExperiment object","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-methods.html","id":"accessors","dir":"Reference","previous_headings":"","what":"Accessors","title":"Accessing and modifying information in MultiAssayExperiment — MultiAssayExperiment-methods","text":"Eponymous names accessing MultiAssayExperiment slots exception ExperimentList accessor named experiments. colData: Access colData slot sampleMap: Access sampleMap slot experiments: Access ExperimentList slot [[: Access ExperimentList slot $: Access column colData drops: Get vector dropped ExperimentList names","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-methods.html","id":"setters","dir":"Reference","previous_headings":"","what":"Setters","title":"Accessing and modifying information in MultiAssayExperiment — MultiAssayExperiment-methods","text":"Setter method values (.e., 'function(x) <- value'): experiments<-: ExperimentList object containing experiment data supported classes sampleMap<-: DataFrame object relating samples biological units assays colData<-: DataFrame object describing biological units metadata<-: list object metadata [[<-: Equivalent experiments<- setter method convenience $<-: vector replace indicated column colData drops<-: Trace ExperimentList names removed","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Accessing and modifying information in MultiAssayExperiment — MultiAssayExperiment-methods","text":"","code":"## Load example MultiAssayExperiment example(MultiAssayExperiment) #> #> MltAsE> ## Run the example ExperimentList #> MltAsE> example(\"ExperimentList\") #> #> ExprmL> ## Create an empty ExperimentList instance #> ExprmL> ExperimentList() #> ExperimentList class object of length 0: #> #> ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class #> ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000294241\", \"ENST00000355076\", #> ExprmL+ \"ENST00000383706\",\"ENST00000234812\", \"ENST00000383323\"), #> ExprmL+ c(\"array1\", \"array2\", \"array3\", \"array4\") #> ExprmL+ )) #> #> ExprmL> colDat <- data.frame(slope53 = rnorm(4), #> ExprmL+ row.names = c(\"array1\", \"array2\", \"array3\", \"array4\")) #> #> ExprmL> ## SummarizedExperiment constructor #> ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, #> ExprmL+ colData = colDat) #> #> ExprmL> ## Create a sample methylation dataset #> ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000355076\", \"ENST00000383706\", #> ExprmL+ \"ENST00000383323\", \"ENST00000234812\", \"ENST00000294241\"), #> ExprmL+ c(\"methyl1\", \"methyl2\", \"methyl3\", #> ExprmL+ \"methyl4\", \"methyl5\") #> ExprmL+ )) #> #> ExprmL> ## Create a sample RNASeqGene dataset #> ExprmL> rnadat <- matrix( #> ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507, #> ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), #> ExprmL+ ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"XIST\", \"RPS4Y1\", \"KDM5D\", \"ENST00000383323\", \"ENST00000234812\"), #> ExprmL+ c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\") #> ExprmL+ )) #> #> ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame #> ExprmL> rangedat <- data.frame(chr=\"chr2\", start = 11:15, end = 12:16, #> ExprmL+ strand = c(\"+\", \"-\", \"+\", \"*\", \".\"), #> ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), #> ExprmL+ row.names = c(paste0(\"ENST\", \"00000\", 135411:135414), \"ENST00000383323\")) #> #> ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) #> #> ExprmL> ## Combine to a named list and call the ExperimentList constructor function #> ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, #> ExprmL+ GISTIC = rangeSE) #> #> ExprmL> ## Use the ExperimentList constructor #> ExprmL> ExpList <- ExperimentList(assayList) #> #> MltAsE> ## Create sample maps for each experiment #> MltAsE> exprmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"array1\", \"array2\", \"array3\", \"array4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> methylmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> rnamap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\"), #> MltAsE+ colname = c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> gistmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Bob\", \"Jill\"), #> MltAsE+ colname = c(\"samp0\", \"samp1\", \"samp2\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> ## Combine as a named list and convert to a DataFrame #> MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap, #> MltAsE+ RNASeqGene = rnamap, GISTIC = gistmap) #> #> MltAsE> ## Create a sampleMap #> MltAsE> sampMap <- listToMap(maplist) #> #> MltAsE> ## Create an example phenotype data #> MltAsE> colDat <- data.frame(sex = c(\"M\", \"F\", \"M\", \"F\"), age = 38:41, #> MltAsE+ row.names = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\")) #> #> MltAsE> ## Create a MultiAssayExperiment instance #> MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat, #> MltAsE+ sampleMap = sampMap) ## Access the sampleMap sampleMap(mae) #> DataFrame with 16 rows and 3 columns #> assay primary colname #> #> 1 Affy Jack array1 #> 2 Affy Jill array2 #> 3 Affy Barbara array3 #> 4 Affy Bob array4 #> 5 Methyl450k Jack methyl1 #> ... ... ... ... #> 12 RNASeqGene Bob samparray3 #> 13 RNASeqGene Barbara samparray4 #> 14 GISTIC Jack samp0 #> 15 GISTIC Bob samp1 #> 16 GISTIC Jill samp2 ## Replacement method for a MultiAssayExperiment sampleMap sampleMap(mae) <- S4Vectors::DataFrame() #> harmonizing input: #> removing 4 colData rownames not in sampleMap 'primary' ## Access the ExperimentList experiments(mae) #> ExperimentList class object of length 0: #> ## Replace with an empty ExperimentList experiments(mae) <- ExperimentList() ## Access the metadata metadata(mae) #> list() ## Replace metadata with a list metadata(mae) <- list(runDate = format(Sys.time(), \"%B %d, %Y\")) ## Access the colData colData(mae) #> DataFrame with 0 rows and 2 columns ## Access a column in colData mae$age #> integer(0) ## Replace a column in colData mae$age <- mae$age + 1"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-package.html","id":null,"dir":"Reference","previous_headings":"","what":"MultiAssayExperiment: Build an integrative multi-assay container — MultiAssayExperiment-package","title":"MultiAssayExperiment: Build an integrative multi-assay container — MultiAssayExperiment-package","text":"MultiAssayExperiment allows manipulation related multiassay datasets partially overlapping samples, associated metadata level entire study, level \"biological unit\". biological unit may patient, plant, yeast strain, etc.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"MultiAssayExperiment: Build an integrative multi-assay container — MultiAssayExperiment-package","text":"package hierarchy information: study experiments samples","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MultiAssayExperiment: Build an integrative multi-assay container — MultiAssayExperiment-package","text":"Maintainer: Marcel Ramos marcel.ramos@roswellpark.org (ORCID) Authors: Martin Morgan [contributor] Vincent J Carey [contributor] Levi Waldron lwaldron.research@gmail.com contributors: Lori Shepherd [contributor] Hervé Pagès [contributor] MultiAssay SIG biocmultiassay@googlegroups.com [contributor]","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html","id":null,"dir":"Reference","previous_headings":"","what":"Construct an integrative representation of multi-omic data with MultiAssayExperiment — MultiAssayExperiment","title":"Construct an integrative representation of multi-omic data with MultiAssayExperiment — MultiAssayExperiment","text":"constructor function MultiAssayExperiment combines multiple data elements different hierarchies data (study, experiments, samples). can create instances neither sampleMap colData set provided. Please see MultiAssayExperiment API documentation information.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Construct an integrative representation of multi-omic data with MultiAssayExperiment — MultiAssayExperiment","text":"","code":"MultiAssayExperiment( experiments = ExperimentList(), colData = S4Vectors::DataFrame(), sampleMap = S4Vectors::DataFrame(assay = factor(), primary = character(), colname = character()), metadata = list(), drops = list() )"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Construct an integrative representation of multi-omic data with MultiAssayExperiment — MultiAssayExperiment","text":"experiments list ExperimentList combined experiments colData DataFrame data.frame characteristics biological units sampleMap DataFrame data.frame assay names, sample identifiers, colname samples metadata optional argument \"\" class (usually list) content describing experiments drops list unmatched information (included subsetting)","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Construct an integrative representation of multi-omic data with MultiAssayExperiment — MultiAssayExperiment","text":"MultiAssayExperiment object can store experiment phenotype data","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html","id":"coldata","dir":"Reference","previous_headings":"","what":"colData","title":"Construct an integrative representation of multi-omic data with MultiAssayExperiment — MultiAssayExperiment","text":"colData input can either DataFrame data.frame subsequent coercion DataFrame. rownames colData must match colnames experiments sampleMap provided.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html","id":"experiments","dir":"Reference","previous_headings":"","what":"experiments","title":"Construct an integrative representation of multi-omic data with MultiAssayExperiment — MultiAssayExperiment","text":"experiments input can class SimpleList list. input becomes ExperimentList. element input list List must named, rectangular two dimensions, dimnames.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html","id":"samplemap","dir":"Reference","previous_headings":"","what":"sampleMap","title":"Construct an integrative representation of multi-omic data with MultiAssayExperiment — MultiAssayExperiment","text":"sampleMap can either input DataFrame data.frame eventual coercion DataFrame. sampleMap relates biological units biological measurements within assay. row sampleMap single link. standard column names sampleMap \"assay\", \"primary\", \"colname\". Note \"assay\" column factor corresponding names experiment ExperimentList. case names match sampleMap experiments, documented experiments sampleMap take precedence experiments dropped harmonization procedure. constructor function generate sampleMap case provided method may 'safer' alternative creating MultiAssayExperiment (long rownames identical colData, provided). empty sampleMap may produce empty experiments levels \"assay\" factor sampleMap match names ExperimentList.","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Construct an integrative representation of multi-omic data with MultiAssayExperiment — MultiAssayExperiment","text":"","code":"## Run the example ExperimentList example(\"ExperimentList\") #> #> ExprmL> ## Create an empty ExperimentList instance #> ExprmL> ExperimentList() #> ExperimentList class object of length 0: #> #> ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class #> ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000294241\", \"ENST00000355076\", #> ExprmL+ \"ENST00000383706\",\"ENST00000234812\", \"ENST00000383323\"), #> ExprmL+ c(\"array1\", \"array2\", \"array3\", \"array4\") #> ExprmL+ )) #> #> ExprmL> colDat <- data.frame(slope53 = rnorm(4), #> ExprmL+ row.names = c(\"array1\", \"array2\", \"array3\", \"array4\")) #> #> ExprmL> ## SummarizedExperiment constructor #> ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, #> ExprmL+ colData = colDat) #> #> ExprmL> ## Create a sample methylation dataset #> ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000355076\", \"ENST00000383706\", #> ExprmL+ \"ENST00000383323\", \"ENST00000234812\", \"ENST00000294241\"), #> ExprmL+ c(\"methyl1\", \"methyl2\", \"methyl3\", #> ExprmL+ \"methyl4\", \"methyl5\") #> ExprmL+ )) #> #> ExprmL> ## Create a sample RNASeqGene dataset #> ExprmL> rnadat <- matrix( #> ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507, #> ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), #> ExprmL+ ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"XIST\", \"RPS4Y1\", \"KDM5D\", \"ENST00000383323\", \"ENST00000234812\"), #> ExprmL+ c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\") #> ExprmL+ )) #> #> ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame #> ExprmL> rangedat <- data.frame(chr=\"chr2\", start = 11:15, end = 12:16, #> ExprmL+ strand = c(\"+\", \"-\", \"+\", \"*\", \".\"), #> ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), #> ExprmL+ row.names = c(paste0(\"ENST\", \"00000\", 135411:135414), \"ENST00000383323\")) #> #> ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) #> #> ExprmL> ## Combine to a named list and call the ExperimentList constructor function #> ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, #> ExprmL+ GISTIC = rangeSE) #> #> ExprmL> ## Use the ExperimentList constructor #> ExprmL> ExpList <- ExperimentList(assayList) ## Create sample maps for each experiment exprmap <- data.frame( primary = c(\"Jack\", \"Jill\", \"Barbara\", \"Bob\"), colname = c(\"array1\", \"array2\", \"array3\", \"array4\"), stringsAsFactors = FALSE) methylmap <- data.frame( primary = c(\"Jack\", \"Jack\", \"Jill\", \"Barbara\", \"Bob\"), colname = c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\"), stringsAsFactors = FALSE) rnamap <- data.frame( primary = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\"), colname = c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\"), stringsAsFactors = FALSE) gistmap <- data.frame( primary = c(\"Jack\", \"Bob\", \"Jill\"), colname = c(\"samp0\", \"samp1\", \"samp2\"), stringsAsFactors = FALSE) ## Combine as a named list and convert to a DataFrame maplist <- list(Affy = exprmap, Methyl450k = methylmap, RNASeqGene = rnamap, GISTIC = gistmap) ## Create a sampleMap sampMap <- listToMap(maplist) ## Create an example phenotype data colDat <- data.frame(sex = c(\"M\", \"F\", \"M\", \"F\"), age = 38:41, row.names = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\")) ## Create a MultiAssayExperiment instance mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat, sampleMap = sampMap)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperimentToMAF.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert MultiAssayExperiment to MAF class — MultiAssayExperimentToMAF","title":"Convert MultiAssayExperiment to MAF class — MultiAssayExperimentToMAF","text":"Take MultiAssayExperiment object specific mutation assays convert maftools representation. names provided via synAssay nonSynAssay must match exactly assays MultiAssayExperiment.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperimentToMAF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert MultiAssayExperiment to MAF class — MultiAssayExperimentToMAF","text":"","code":"MultiAssayExperimentToMAF(x, synAssay = \"maf_syn\", nonSynAssay = \"maf_nonSyn\")"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperimentToMAF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert MultiAssayExperiment to MAF class — MultiAssayExperimentToMAF","text":"x MultiAssayExperiment object synAssay character(1) name ExperimentList element MultiAssayExperiment identifies synonymous variant classifications. nonSynAssay character(1) name ExperimentList element MultiAssayExperiment identifies non-synonymous variant classifications.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/hasAssay.html","id":null,"dir":"Reference","previous_headings":"","what":"Checking assay method for any class — hasAssay","title":"Checking assay method for any class — hasAssay","text":"hasAssay function intended developers like include new classes MultiAssayExperiment instance. checks methods tables assay function specified class argument.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/hasAssay.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checking assay method for any class — hasAssay","text":"","code":"hasAssay(object)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/hasAssay.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checking assay method for any class — hasAssay","text":"object MultiAssayExperiment named list object instance","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/hasAssay.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checking assay method for any class — hasAssay","text":"logical value indicating method availability","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/hasAssay.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checking assay method for any class — hasAssay","text":"","code":"lst <- structure(list(), .Names=character()) hasAssay(lst) #> [1] TRUE"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/mapToList.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert map from data.frame or DataFrame to list and vice versa — listToMap","title":"Convert map from data.frame or DataFrame to list and vice versa — listToMap","text":"mapToList function provides convenient way reordering data.frame list. listToMap function opposite taking list converting DataFrame.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/mapToList.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert map from data.frame or DataFrame to list and vice versa — listToMap","text":"","code":"listToMap(listmap, fill = TRUE) mapToList(dfmap, assayCol = \"assay\")"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/mapToList.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert map from data.frame or DataFrame to list and vice versa — listToMap","text":"listmap named list object containing DataFrames \"primary\" \"colname\" columns fill logical(1) Whether fill map empty DataFrame empty elements present input list dfmap data.frame DataFrame object identifiers first column assayCol character vector length one indicating assay names column","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/mapToList.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert map from data.frame or DataFrame to list and vice versa — listToMap","text":"DataFrame class object names list object DataFrames assay","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/mapToList.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Convert map from data.frame or DataFrame to list and vice versa — listToMap","text":"listToMap(): inverse listToMap operation","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/mapToList.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert map from data.frame or DataFrame to list and vice versa — listToMap","text":"","code":"example(\"MultiAssayExperiment\") #> #> MltAsE> ## Run the example ExperimentList #> MltAsE> example(\"ExperimentList\") #> #> ExprmL> ## Create an empty ExperimentList instance #> ExprmL> ExperimentList() #> ExperimentList class object of length 0: #> #> ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class #> ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000294241\", \"ENST00000355076\", #> ExprmL+ \"ENST00000383706\",\"ENST00000234812\", \"ENST00000383323\"), #> ExprmL+ c(\"array1\", \"array2\", \"array3\", \"array4\") #> ExprmL+ )) #> #> ExprmL> colDat <- data.frame(slope53 = rnorm(4), #> ExprmL+ row.names = c(\"array1\", \"array2\", \"array3\", \"array4\")) #> #> ExprmL> ## SummarizedExperiment constructor #> ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, #> ExprmL+ colData = colDat) #> #> ExprmL> ## Create a sample methylation dataset #> ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000355076\", \"ENST00000383706\", #> ExprmL+ \"ENST00000383323\", \"ENST00000234812\", \"ENST00000294241\"), #> ExprmL+ c(\"methyl1\", \"methyl2\", \"methyl3\", #> ExprmL+ \"methyl4\", \"methyl5\") #> ExprmL+ )) #> #> ExprmL> ## Create a sample RNASeqGene dataset #> ExprmL> rnadat <- matrix( #> ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507, #> ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), #> ExprmL+ ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"XIST\", \"RPS4Y1\", \"KDM5D\", \"ENST00000383323\", \"ENST00000234812\"), #> ExprmL+ c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\") #> ExprmL+ )) #> #> ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame #> ExprmL> rangedat <- data.frame(chr=\"chr2\", start = 11:15, end = 12:16, #> ExprmL+ strand = c(\"+\", \"-\", \"+\", \"*\", \".\"), #> ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), #> ExprmL+ row.names = c(paste0(\"ENST\", \"00000\", 135411:135414), \"ENST00000383323\")) #> #> ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) #> #> ExprmL> ## Combine to a named list and call the ExperimentList constructor function #> ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, #> ExprmL+ GISTIC = rangeSE) #> #> ExprmL> ## Use the ExperimentList constructor #> ExprmL> ExpList <- ExperimentList(assayList) #> #> MltAsE> ## Create sample maps for each experiment #> MltAsE> exprmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"array1\", \"array2\", \"array3\", \"array4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> methylmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> rnamap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\"), #> MltAsE+ colname = c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> gistmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Bob\", \"Jill\"), #> MltAsE+ colname = c(\"samp0\", \"samp1\", \"samp2\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> ## Combine as a named list and convert to a DataFrame #> MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap, #> MltAsE+ RNASeqGene = rnamap, GISTIC = gistmap) #> #> MltAsE> ## Create a sampleMap #> MltAsE> sampMap <- listToMap(maplist) #> #> MltAsE> ## Create an example phenotype data #> MltAsE> colDat <- data.frame(sex = c(\"M\", \"F\", \"M\", \"F\"), age = 38:41, #> MltAsE+ row.names = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\")) #> #> MltAsE> ## Create a MultiAssayExperiment instance #> MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat, #> MltAsE+ sampleMap = sampMap) ## Create a sampleMap from a list using the listToMap function sampMap <- listToMap(maplist) ## The inverse operation is also available maplist <- mapToList(sampMap)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/miniACC.html","id":null,"dir":"Reference","previous_headings":"","what":"Adrenocortical Carcinoma (ACC) MultiAssayExperiment — miniACC","title":"Adrenocortical Carcinoma (ACC) MultiAssayExperiment — miniACC","text":"MultiAssayExperiment object providing reduced version TCGA ACC dataset 92 patients. RNA-seq, copy number, somatic mutations included genes whose proteins included reverse-phase protein array. MicroRNA-seq dataset also included, infrequently expressed microRNA removed. Clinical, pathological, subtype information provided colData(miniACC), additional details provided metadata(miniACC).","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/miniACC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adrenocortical Carcinoma (ACC) MultiAssayExperiment — miniACC","text":"","code":"data(\"miniACC\")"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/miniACC.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Adrenocortical Carcinoma (ACC) MultiAssayExperiment — miniACC","text":"MultiAssayExperiment 5 experiments, providing: RNASeq2GeneNorm RNA-seq count data: ExpressionSet 198 rows 79 columns gistict Reccurent copy number lesions identified GISTIC2: SummarizedExperiment 198 rows 90 columns RPPAArray Reverse Phase Protein Array: ExpressionSet 33 rows 46 columns. Rows indexed genes, protein annotations available featureData(miniACC[[\"RPPAArray\"]]). source annotations noted abstract(miniACC[[\"RPPAArray\"]]) Mutations Somatic mutations: matrix 223 rows 90 columns. 1 kind non-silent mutation, zero silent (synonymous) mutation. miRNASeqGene microRNA sequencing: ExpressionSet 471 rows 80 columns. Rows least 5 counts least 5 samples removed.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/miniACC.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Adrenocortical Carcinoma (ACC) MultiAssayExperiment — miniACC","text":"https://github.com/waldronlab/multiassayexperiment-tcga","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/miniACC.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Adrenocortical Carcinoma (ACC) MultiAssayExperiment — miniACC","text":"Zheng S et al.: Comprehensive Pan-Genomic Characterization Adrenocortical Carcinoma. Cancer Cell 2016, 29:723-736.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/miniACC.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Adrenocortical Carcinoma (ACC) MultiAssayExperiment — miniACC","text":"Levi Waldron lwaldron.research@gmail.com","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/miniACC.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adrenocortical Carcinoma (ACC) MultiAssayExperiment — miniACC","text":"","code":"data(\"miniACC\") metadata(miniACC) #> $title #> [1] \"Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma\" #> #> $PMID #> [1] \"27165744\" #> #> $sourceURL #> [1] \"http://s3.amazonaws.com/multiassayexperiments/accMAEO.rds\" #> #> $RPPAfeatureDataURL #> [1] \"http://genomeportal.stanford.edu/pan-tcga/show_target_selection_file?filename=Allprotein.txt\" #> #> $colDataExtrasURL #> [1] \"http://www.cell.com/cms/attachment/2062093088/2063584534/mmc3.xlsx\" #> colnames(colData(miniACC)) #> [1] \"patientID\" #> [2] \"years_to_birth\" #> [3] \"vital_status\" #> [4] \"days_to_death\" #> [5] \"days_to_last_followup\" #> [6] \"tumor_tissue_site\" #> [7] \"pathologic_stage\" #> [8] \"pathology_T_stage\" #> [9] \"pathology_N_stage\" #> [10] \"gender\" #> [11] \"date_of_initial_pathologic_diagnosis\" #> [12] \"radiation_therapy\" #> [13] \"histological_type\" #> [14] \"residual_tumor\" #> [15] \"number_of_lymph_nodes\" #> [16] \"race\" #> [17] \"ethnicity\" #> [18] \"Histology\" #> [19] \"C1A.C1B\" #> [20] \"mRNA_K4\" #> [21] \"MethyLevel\" #> [22] \"miRNA.cluster\" #> [23] \"SCNA.cluster\" #> [24] \"protein.cluster\" #> [25] \"COC\" #> [26] \"OncoSign\" #> [27] \"purity\" #> [28] \"ploidy\" #> [29] \"genome_doublings\" #> [30] \"ADS\" table(miniACC$vital_status) #> #> 0 1 #> 58 34 longFormat( miniACC[\"MAPK3\", , ], colDataCols = c(\"vital_status\", \"days_to_death\") ) #> harmonizing input: #> removing 216 sampleMap rows not in names(experiments) #> DataFrame with 169 rows and 7 columns #> assay primary rowname colname #> #> 1 RNASeq2GeneNorm TCGA-OR-A5J1 MAPK3 TCGA-OR-A5J1-01A-11R-A29S-07 #> 2 RNASeq2GeneNorm TCGA-OR-A5J2 MAPK3 TCGA-OR-A5J2-01A-11R-A29S-07 #> 3 RNASeq2GeneNorm TCGA-OR-A5J3 MAPK3 TCGA-OR-A5J3-01A-11R-A29S-07 #> 4 RNASeq2GeneNorm TCGA-OR-A5J5 MAPK3 TCGA-OR-A5J5-01A-11R-A29S-07 #> 5 RNASeq2GeneNorm TCGA-OR-A5J6 MAPK3 TCGA-OR-A5J6-01A-31R-A29S-07 #> ... ... ... ... ... #> 165 gistict TCGA-PA-A5YG MAPK3 TCGA-PA-A5YG-01A-11D-A29H-01 #> 166 gistict TCGA-PK-A5H9 MAPK3 TCGA-PK-A5H9-01A-11D-A29H-01 #> 167 gistict TCGA-PK-A5HA MAPK3 TCGA-PK-A5HA-01A-11D-A29H-01 #> 168 gistict TCGA-PK-A5HB MAPK3 TCGA-PK-A5HB-01A-11D-A29H-01 #> 169 gistict TCGA-PK-A5HC MAPK3 TCGA-PK-A5HC-01A-11D-A309-01 #> value vital_status days_to_death #> #> 1 946.681 1 1355 #> 2 1699.382 1 1677 #> 3 2347.243 0 NA #> 4 1299.156 1 365 #> 5 2543.424 0 NA #> ... ... ... ... #> 165 1 0 NA #> 166 0 0 NA #> 167 0 0 NA #> 168 0 0 NA #> 169 1 0 NA wideFormat( miniACC[\"MAPK3\", , ], colDataCols = c(\"vital_status\", \"days_to_death\") ) #> harmonizing input: #> removing 216 sampleMap rows not in names(experiments) #> DataFrame with 92 rows and 5 columns #> primary vital_status days_to_death RNASeq2GeneNorm_MAPK3 gistict_MAPK3 #> #> 1 TCGA-OR-A5J1 1 1355 946.681 0 #> 2 TCGA-OR-A5J2 1 1677 1699.382 0 #> 3 TCGA-OR-A5J3 0 NA 2347.243 1 #> 4 TCGA-OR-A5J4 1 423 NA 0 #> 5 TCGA-OR-A5J5 1 365 1299.156 1 #> ... ... ... ... ... ... #> 88 TCGA-PK-A5H9 0 NA 1013.47 0 #> 89 TCGA-PK-A5HA 0 NA 2446.12 0 #> 90 TCGA-PK-A5HB 0 NA 1463.31 0 #> 91 TCGA-PK-A5HC 0 NA NA 1 #> 92 TCGA-P6-A5OG 1 383 1310.88 -1"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/prepMultiAssay.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare a MultiAssayExperiment instance — prepMultiAssay","title":"Prepare a MultiAssayExperiment instance — prepMultiAssay","text":"purpose helper function faciltate creation MultiAssayExperiment object detecting inconsistencies types names either ExperimentList, colData, sampleMap.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/prepMultiAssay.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare a MultiAssayExperiment instance — prepMultiAssay","text":"","code":"prepMultiAssay(ExperimentList, colData, sampleMap, ...)"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/prepMultiAssay.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare a MultiAssayExperiment instance — prepMultiAssay","text":"ExperimentList list combined experiments colData DataFrame phenotype data participants sampleMap DataFrame sample identifiers, assay samples, assay names ... Optional arguments MultiAssayExperiment constructor function metadata drops.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/prepMultiAssay.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare a MultiAssayExperiment instance — prepMultiAssay","text":"list containing essential components MultiAssayExperiment well \"drops\" metadata element indicates non-matched names. names resulting list correspond arguments MultiAssayExperiment constructor function.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/prepMultiAssay.html","id":"checks","dir":"Reference","previous_headings":"","what":"Checks","title":"Prepare a MultiAssayExperiment instance — prepMultiAssay","text":"prepMultiAssay function checks columns sampleMap character. checks names lengths match ExperimentList unique assay names sampleMap. ExperimentList names assay names differ case duplicated, function standardize names lowercase. names matched colname column sampleMap colnames ExperimentList, unmatched dropped found \"drops\" element resulting list. Names \"primary\" column sampleMap, matched colData. Unmatched \"primary\" column rows dropped sampleMap. Suggestions name fixes either ExperimentList colnames made necessary.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/prepMultiAssay.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare a MultiAssayExperiment instance — prepMultiAssay","text":"","code":"## Run example example(\"MultiAssayExperiment\") #> #> MltAsE> ## Run the example ExperimentList #> MltAsE> example(\"ExperimentList\") #> #> ExprmL> ## Create an empty ExperimentList instance #> ExprmL> ExperimentList() #> ExperimentList class object of length 0: #> #> ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class #> ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000294241\", \"ENST00000355076\", #> ExprmL+ \"ENST00000383706\",\"ENST00000234812\", \"ENST00000383323\"), #> ExprmL+ c(\"array1\", \"array2\", \"array3\", \"array4\") #> ExprmL+ )) #> #> ExprmL> colDat <- data.frame(slope53 = rnorm(4), #> ExprmL+ row.names = c(\"array1\", \"array2\", \"array3\", \"array4\")) #> #> ExprmL> ## SummarizedExperiment constructor #> ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, #> ExprmL+ colData = colDat) #> #> ExprmL> ## Create a sample methylation dataset #> ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000355076\", \"ENST00000383706\", #> ExprmL+ \"ENST00000383323\", \"ENST00000234812\", \"ENST00000294241\"), #> ExprmL+ c(\"methyl1\", \"methyl2\", \"methyl3\", #> ExprmL+ \"methyl4\", \"methyl5\") #> ExprmL+ )) #> #> ExprmL> ## Create a sample RNASeqGene dataset #> ExprmL> rnadat <- matrix( #> ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507, #> ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), #> ExprmL+ ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"XIST\", \"RPS4Y1\", \"KDM5D\", \"ENST00000383323\", \"ENST00000234812\"), #> ExprmL+ c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\") #> ExprmL+ )) #> #> ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame #> ExprmL> rangedat <- data.frame(chr=\"chr2\", start = 11:15, end = 12:16, #> ExprmL+ strand = c(\"+\", \"-\", \"+\", \"*\", \".\"), #> ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), #> ExprmL+ row.names = c(paste0(\"ENST\", \"00000\", 135411:135414), \"ENST00000383323\")) #> #> ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) #> #> ExprmL> ## Combine to a named list and call the ExperimentList constructor function #> ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, #> ExprmL+ GISTIC = rangeSE) #> #> ExprmL> ## Use the ExperimentList constructor #> ExprmL> ExpList <- ExperimentList(assayList) #> #> MltAsE> ## Create sample maps for each experiment #> MltAsE> exprmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"array1\", \"array2\", \"array3\", \"array4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> methylmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> rnamap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\"), #> MltAsE+ colname = c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> gistmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Bob\", \"Jill\"), #> MltAsE+ colname = c(\"samp0\", \"samp1\", \"samp2\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> ## Combine as a named list and convert to a DataFrame #> MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap, #> MltAsE+ RNASeqGene = rnamap, GISTIC = gistmap) #> #> MltAsE> ## Create a sampleMap #> MltAsE> sampMap <- listToMap(maplist) #> #> MltAsE> ## Create an example phenotype data #> MltAsE> colDat <- data.frame(sex = c(\"M\", \"F\", \"M\", \"F\"), age = 38:41, #> MltAsE+ row.names = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\")) #> #> MltAsE> ## Create a MultiAssayExperiment instance #> MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat, #> MltAsE+ sampleMap = sampMap) ## Check if there are any inconsistencies within the different names preparedMAE <- prepMultiAssay(ExpList, colDat, sampMap) ## Results in a list of components for the MultiAssayExperiment constructor ## function MultiAssayExperiment(preparedMAE$experiments, preparedMAE$colData, preparedMAE$sampleMap) #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 5 rows and 4 columns #> [2] Methyl450k: matrix with 5 rows and 5 columns #> [3] RNASeqGene: matrix with 5 rows and 4 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 3 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Alternatively, use the do.call function do.call(MultiAssayExperiment, preparedMAE) #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 5 rows and 4 columns #> [2] Methyl450k: matrix with 5 rows and 5 columns #> [3] RNASeqGene: matrix with 5 rows and 4 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 3 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Click function name see documentation. S4Vectors: DataFrame","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/reexports.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Objects exported from other packages — reexports","text":"","code":"DataFrame() #> DataFrame with 0 rows and 0 columns"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/subsetBy.html","id":null,"dir":"Reference","previous_headings":"","what":"Subsetting a MultiAssayExperiment object — subsetBy","title":"Subsetting a MultiAssayExperiment object — subsetBy","text":"set functions extracting dividing MultiAssayExperiment","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/subsetBy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subsetting a MultiAssayExperiment object — subsetBy","text":"","code":"subsetByRow(x, y, ...) subsetByColData(x, y) subsetByColumn(x, y) subsetByAssay(x, y) # S4 method for class 'ExperimentList,ANY' subsetByRow(x, y, ...) # S4 method for class 'ExperimentList,list' subsetByRow(x, y) # S4 method for class 'ExperimentList,List' subsetByRow(x, y) # S4 method for class 'ExperimentList,logical' subsetByRow(x, y) # S4 method for class 'ExperimentList,list' subsetByColumn(x, y) # S4 method for class 'ExperimentList,List' subsetByColumn(x, y) # S4 method for class 'ExperimentList,logical' subsetByColumn(x, y) # S4 method for class 'ExperimentList' subsetByAssay(x, y) # S4 method for class 'MultiAssayExperiment,ANY' subsetByColData(x, y) # S4 method for class 'MultiAssayExperiment,character' subsetByColData(x, y) # S4 method for class 'MultiAssayExperiment,ANY' subsetByRow(x, y, ...) # S4 method for class 'MultiAssayExperiment,ANY' subsetByColumn(x, y) # S4 method for class 'MultiAssayExperiment' subsetByAssay(x, y) # S4 method for class 'MultiAssayExperiment,ANY,ANY,ANY' x[i, j, k, ..., drop = FALSE] # S4 method for class 'MultiAssayExperiment,ANY,ANY' x[[i, j, ...]] # S4 method for class 'MultiAssayExperiment,ANY,ANY' x[[i, j, ...]] <- value # S4 method for class 'MultiAssayExperiment,ANY,ANY,ANY' x[i, j, ...] <- value"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/subsetBy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subsetting a MultiAssayExperiment object — subsetBy","text":"x MultiAssayExperiment ExperimentList y argument used subsetting, can character, logical, integer, list List vector ... Additional arguments passed lower level functions. Either character, integer, logical GRanges object subsetting rows j Either character, logical, numeric vector subsetting colData rows. See details information. k Either character, logical, numeric vector subsetting assays drop logical (default FALSE) whether drop empty assay elements ExperimentList value assay compatible MultiAssayExperiment API","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/subsetBy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subsetting a MultiAssayExperiment object — subsetBy","text":"subsetBy* operations endomorphic return either MultiAssayExperiment ExperimentList depending input.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/subsetBy.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Subsetting a MultiAssayExperiment object — subsetBy","text":"Subsetting MultiAssayExperiment j index can yield call either subsetByColData subsetByColumn. vector inputs, subset applied colData rows. List-type inputs, List applied elements ExperimentList. order subsetting elements List must match ExperimentList MultiAssayExperiment. subsetBycolData: Select biological units vector input types subsetByColumn: Select observations assay assay subsetByRow: Select rows assay assay subsetByAssay: Select experiments","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/subsetBy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subsetting a MultiAssayExperiment object — subsetBy","text":"","code":"## Load the example MultiAssayExperiment example(\"MultiAssayExperiment\") #> #> MltAsE> ## Run the example ExperimentList #> MltAsE> example(\"ExperimentList\") #> #> ExprmL> ## Create an empty ExperimentList instance #> ExprmL> ExperimentList() #> ExperimentList class object of length 0: #> #> ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class #> ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000294241\", \"ENST00000355076\", #> ExprmL+ \"ENST00000383706\",\"ENST00000234812\", \"ENST00000383323\"), #> ExprmL+ c(\"array1\", \"array2\", \"array3\", \"array4\") #> ExprmL+ )) #> #> ExprmL> colDat <- data.frame(slope53 = rnorm(4), #> ExprmL+ row.names = c(\"array1\", \"array2\", \"array3\", \"array4\")) #> #> ExprmL> ## SummarizedExperiment constructor #> ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, #> ExprmL+ colData = colDat) #> #> ExprmL> ## Create a sample methylation dataset #> ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"ENST00000355076\", \"ENST00000383706\", #> ExprmL+ \"ENST00000383323\", \"ENST00000234812\", \"ENST00000294241\"), #> ExprmL+ c(\"methyl1\", \"methyl2\", \"methyl3\", #> ExprmL+ \"methyl4\", \"methyl5\") #> ExprmL+ )) #> #> ExprmL> ## Create a sample RNASeqGene dataset #> ExprmL> rnadat <- matrix( #> ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507, #> ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), #> ExprmL+ ncol = 4, #> ExprmL+ dimnames = list( #> ExprmL+ c(\"XIST\", \"RPS4Y1\", \"KDM5D\", \"ENST00000383323\", \"ENST00000234812\"), #> ExprmL+ c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\") #> ExprmL+ )) #> #> ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame #> ExprmL> rangedat <- data.frame(chr=\"chr2\", start = 11:15, end = 12:16, #> ExprmL+ strand = c(\"+\", \"-\", \"+\", \"*\", \".\"), #> ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), #> ExprmL+ row.names = c(paste0(\"ENST\", \"00000\", 135411:135414), \"ENST00000383323\")) #> #> ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) #> #> ExprmL> ## Combine to a named list and call the ExperimentList constructor function #> ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, #> ExprmL+ GISTIC = rangeSE) #> #> ExprmL> ## Use the ExperimentList constructor #> ExprmL> ExpList <- ExperimentList(assayList) #> #> MltAsE> ## Create sample maps for each experiment #> MltAsE> exprmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"array1\", \"array2\", \"array3\", \"array4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> methylmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jack\", \"Jill\", \"Barbara\", \"Bob\"), #> MltAsE+ colname = c(\"methyl1\", \"methyl2\", \"methyl3\", \"methyl4\", \"methyl5\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> rnamap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\"), #> MltAsE+ colname = c(\"samparray1\", \"samparray2\", \"samparray3\", \"samparray4\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> gistmap <- data.frame( #> MltAsE+ primary = c(\"Jack\", \"Bob\", \"Jill\"), #> MltAsE+ colname = c(\"samp0\", \"samp1\", \"samp2\"), #> MltAsE+ stringsAsFactors = FALSE) #> #> MltAsE> ## Combine as a named list and convert to a DataFrame #> MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap, #> MltAsE+ RNASeqGene = rnamap, GISTIC = gistmap) #> #> MltAsE> ## Create a sampleMap #> MltAsE> sampMap <- listToMap(maplist) #> #> MltAsE> ## Create an example phenotype data #> MltAsE> colDat <- data.frame(sex = c(\"M\", \"F\", \"M\", \"F\"), age = 38:41, #> MltAsE+ row.names = c(\"Jack\", \"Jill\", \"Bob\", \"Barbara\")) #> #> MltAsE> ## Create a MultiAssayExperiment instance #> MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat, #> MltAsE+ sampleMap = sampMap) ## Using experiment names subsetByAssay(mae, \"Affy\") #> Warning: 'experiments' dropped; see 'drops()' #> harmonizing input: #> removing 12 sampleMap rows not in names(experiments) #> A MultiAssayExperiment object of 1 listed #> experiment with a user-defined name and respective class. #> Containing an ExperimentList class object of length 1: #> [1] Affy: SummarizedExperiment with 5 rows and 4 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Using numeric indices subsetByAssay(mae, 1:2) #> Warning: 'experiments' dropped; see 'drops()' #> harmonizing input: #> removing 7 sampleMap rows not in names(experiments) #> A MultiAssayExperiment object of 2 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 2: #> [1] Affy: SummarizedExperiment with 5 rows and 4 columns #> [2] Methyl450k: matrix with 5 rows and 5 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Using a logical vector subsetByAssay(mae, c(TRUE, FALSE, TRUE)) #> Warning: 'experiments' dropped; see 'drops()' #> harmonizing input: #> removing 5 sampleMap rows not in names(experiments) #> A MultiAssayExperiment object of 3 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 3: #> [1] Affy: SummarizedExperiment with 5 rows and 4 columns #> [2] RNASeqGene: matrix with 5 rows and 4 columns #> [3] GISTIC: RangedSummarizedExperiment with 5 rows and 3 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Subset by character vector (Jack) subsetByColData(mae, \"Jack\") #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 5 rows and 1 columns #> [2] Methyl450k: matrix with 5 rows and 2 columns #> [3] RNASeqGene: matrix with 5 rows and 1 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 1 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Subset by numeric index of colData rows (Jack and Bob) subsetByColData(mae, c(1, 3)) #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 5 rows and 2 columns #> [2] Methyl450k: matrix with 5 rows and 3 columns #> [3] RNASeqGene: matrix with 5 rows and 2 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 2 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Subset by logical indicator of colData rows (Jack and Jill) subsetByColData(mae, c(TRUE, TRUE, FALSE, FALSE)) #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 5 rows and 2 columns #> [2] Methyl450k: matrix with 5 rows and 3 columns #> [3] RNASeqGene: matrix with 5 rows and 2 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 2 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files subsetByColumn(mae, list(Affy = 1:2, Methyl450k = c(3,5,2), RNASeqGene = 2:4, GISTIC = 1)) #> harmonizing input: #> removing 7 sampleMap rows with 'colname' not in colnames of experiments #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 5 rows and 2 columns #> [2] Methyl450k: matrix with 5 rows and 3 columns #> [3] RNASeqGene: matrix with 5 rows and 3 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 1 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files subsetWith <- S4Vectors::mendoapply(`[`, colnames(mae), MoreArgs = list(1:2)) subsetByColumn(mae, subsetWith) #> harmonizing input: #> removing 8 sampleMap rows with 'colname' not in colnames of experiments #> removing 1 colData rownames not in sampleMap 'primary' #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 5 rows and 2 columns #> [2] Methyl450k: matrix with 5 rows and 2 columns #> [3] RNASeqGene: matrix with 5 rows and 2 columns #> [4] GISTIC: RangedSummarizedExperiment with 5 rows and 2 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Use a GRanges object to subset rows where ranged data present egr <- GenomicRanges::GRanges(seqnames = \"chr2\", IRanges::IRanges(start = 11, end = 13), strand = \"-\") subsetByRow(mae, egr) #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 0 rows and 4 columns #> [2] Methyl450k: matrix with 0 rows and 5 columns #> [3] RNASeqGene: matrix with 0 rows and 4 columns #> [4] GISTIC: RangedSummarizedExperiment with 1 rows and 3 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Use a logical vector (recycling used) subsetByRow(mae, c(TRUE, FALSE)) #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 3 rows and 4 columns #> [2] Methyl450k: matrix with 3 rows and 5 columns #> [3] RNASeqGene: matrix with 3 rows and 4 columns #> [4] GISTIC: RangedSummarizedExperiment with 3 rows and 3 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files ## Use a character vector subsetByRow(mae, \"ENST00000355076\") #> A MultiAssayExperiment object of 4 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 4: #> [1] Affy: SummarizedExperiment with 1 rows and 4 columns #> [2] Methyl450k: matrix with 1 rows and 5 columns #> [3] RNASeqGene: matrix with 0 rows and 4 columns #> [4] GISTIC: RangedSummarizedExperiment with 0 rows and 3 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/upsetSamples.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR — upsetSamples","title":"Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR — upsetSamples","text":"Create generalized Venn Diagram analog sample membership multiple assays, using upset algorithm UpSetR","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/upsetSamples.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR — upsetSamples","text":"","code":"upsetSamples( MultiAssayExperiment, nsets = NULL, sets = names(MultiAssayExperiment), nintersects = NA_integer_, order.by = \"freq\", check.names = FALSE, ... )"},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/upsetSamples.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR — upsetSamples","text":"MultiAssayExperiment MultiAssayExperiment object nsets numeric(1) number sets analyze. specified, sets ignored. sets character() character vector names MultiAssayExperiment use. specified, nsets ignored. nintersects numeric(1) number intersections plot. default, intersections plotted. order.intersections matrix ordered . Options include frequency (entered \"freq\"), degree, order. check.names logical(1) Whether munge names data.frame() constructor (default FALSE). ... parameters passed UpSetR::upset","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/upsetSamples.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR — upsetSamples","text":"Produces visualization set intersections using UpSet matrix design","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/upsetSamples.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR — upsetSamples","text":"function intended provide convenient visualization assay availability configurations MultiAssayExperiment instances. UpSetR::upset function requires data.frame input many parameters tune appearance result. Assay name handling important interpretability.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/upsetSamples.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR — upsetSamples","text":"Vincent J Carey","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/reference/upsetSamples.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR — upsetSamples","text":"","code":"data(miniACC) upsetSamples(miniACC) upsetSamples(miniACC, nsets = 3, nintersects = 3)"},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-30-3","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.30.3","text":"colData<- replacement method now correctly works data.frame value inputs (@drighelli, #330). Updated CITATION information main vignette. Use reshape2::melt instead stats::reshape preserve row names longFormat rownames numeric characters e.g., “1”, ensure stay character converting MultiAssayExperiment longFormat.","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-28-0","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.28.0","text":"Dropped experiments longer kept metadata slot. can seen drops() (@LTLA, #323).","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-28-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.28.0","text":"Checking colnames sampleMap vs ExperimentList robust comparing unique sorted values .","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-26-0","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.26.0","text":"showReplicated displays actual colnames technical replicates assay biological unit. bracket replacement method [<- MultiAssayExperiment now also replaces names right-hand side operation, (@DarioS, #319)","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-26-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.26.0","text":"single assay replacement [[<-, re-ordering assays based value input invalid empty assays present (@danielinteractive, #322). Permuting assays also updates order names MultiAssayExperiment assays sampleMap","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-24-0","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.24.0","text":"replicates provides actual colnames identified replicate observations particular biological unit sampleMap","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-24-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.24.0","text":"Added assay<- replacement method robustifying saveHDF5MultiAssayExperiment plain matrices Use BiocBaseUtils::setSlots avoid warnings triple colon use. Resolve issue colData one column merging two MultiAssayExperiment objects, .e., using c method (@cvanderaa, #315) Increase efficiency colnames rownames methods (@cvanderaa, #314) Make ‘prefix’ inputs consistent saveHDF5MultiAssayExperiment loadHDF5MultiAssayExperiment (@asiyeka, #313) Improve performance replicated method Update wideFormat documentation, replicates present additional sets columns appended produced DataFrame (@DarioS, #312)","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-22-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.22.0","text":"Add data(\"miniACC\") examples removing lazy loading. Class definition prototypes defined cleaner extensibility (@hpages, #306). Doc internal improvments MultiAssayExperimentToMAF synAssay nonSynAssay now require exact assay names MultiAssayExperimentToMAF","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-20-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.20.0","text":"Avoid dropping experiments repeated calls subsetByColData remove harmonization (@cvanderaa, #302) getWithColData suppresses messages natural subsetting operations default verbose = FALSE (@bhagwataditya, #301) getWithColData using old default (drop = TRUE) causing error experiment empty (@danielinteractive, #300). Calls internal .harmonize operation reduced increase memory efficiency, identical experiment colnames present (@LTLA, #299). subsetByColData now errors subscript vectors longer nrow colData (previously warning). colData<- includes check identical row names. , direct replacement colData occurs without harmonization. Added warning empty sampleMap provided constructor function may cause unexpected behavior. Documentation updated include details sampleMap input.","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-18-0","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.18.0","text":"saveHDF5MultiAssayExperiment allows users save data classes (excluding RaggedExperiment) single H5 file (ctb @hpages) Support maftools conversion added MultiAssayExperimentToMAF (ctb @PoisonAlien) renameColname renamePrimary provide renaming facilities column names experiments rownames colData, respectively Users can now rename column names experiments using colnames(mae) <- value replacing colData experiments (including [[<-), new rownames colnames (respectively) checked existing values error given none match Using List objects replace data ExperimentList now supported splitAssay allows users separate / split columns across assays makeHitList facilitator function create logical lists required input splitAssay drop argument subsetting MultiAssayExperiment now FALSE default","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-18-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.18.0","text":"Updated constructor function auto-populate rownames colData missing (@LTLA, #287) metadata now includes names dropped experiments Updated validity checks support array-like classes Dropped experiments tracked metadata","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-16-0","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.16.0","text":"Coercion methods list/List MultiAssayExperiment method now available.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-16-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.16.0","text":"Provide details documentation mergeReplicates Improved documentation accessor function return values, helper function examples (@llrs, #281) Fixed bug using longFormat character assay matrices (@jonocarroll, #282)","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-14-0","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.14.0","text":"exportClass creates number .csv data files exporting data Allow vector input selecting assays longFormat (@lgatto, #266) Updates ‘Using MultiAssayExperiment DelayedMatrix’ vignette","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-14-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.14.0","text":"Warn colData rownames ExperimentList colnames empty (@LTLA #262) Add informative error message ExperimentList (@lgatto, #265) Informative warning dropping ExperimentList element columns (@lwaldron) Fixes constructor functions, MultiAssayExperiment MatchedAssayExperiment (@lgatto, #267 #268, @lwaldron) Add warning j mae[, j, k] longer colData rows Strict argument matching generic methods Updates due class(matrix()) UpsetSamples robust differences names split sampleMap names(ExperimentList) (@jonocarroll, #269) Refactored improved UpsetSamples ExperimentList propagation mcols metadata (@vobencha, #270) Enforcement validObject replacement methods colData sampleMap (@vobencha, #271)","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-12-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.12.0","text":"Improvements main vignette, MultiAssayExperiment class schematic now included (@mtmorgan, #261) Updated documentation upsetSamples function Update code use splitAsList S4Vectors (@hpages) Fixed bug metadata disappearing ExperimentList replacing inside MultiAssayExperiment object (@lawremi, #259) Fixed formatting NEWS file","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-10-0","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.10.0","text":"getWithColData now allows easy extraction experiments (SummarizedExperiment) associated colData data Single bracket replace method implemented MultiAssayExperiment assays","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-10-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.10.0","text":"isEmpty method fixed ExperimentLists containing matrices MultiAssayExperiment now inherits standard Annotated virtual class c method better distinguishes list ExperimentList inputs Improvements .getHits internal method obtaining correct queries row metadata Subsetting mechanism tweaked nothing subsetting NULL rows compared empty rows (.e., character(0L)) Improved README.md","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-8-0","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.8.0","text":"single bracket replacement method [<- added support assignment assay datasets Users can now rename experiments MultiAssayExperiment names(x) <- value replicated mergeReplicates functions refactored improved combining MultiAssayExperiments now possible c function Subsetting MultiAssayExperiment list List type class now returns experiments input order rows, columns, assays","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-8-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.8.0","text":"wideFormat function improvements bug fixes name indicator subsetting BiocGenerics:::replaceSlots used instead replace methods Added tests anyReplicated, c, names<- functions Unit tests added replacement method testing Renamed objects examples brevity descriptiveness Updated importFrom directives Internal sample names check now works non-empty colnames Various documentation improvements listToMap re-written efficiency Various improvements subsetting mechanism subsetByAssay bug fixed using integer index (@vjcitn, #)","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-6-0","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.6.0","text":"DataFrame now exported users (@DarioS, #242) c smarter matching colnames primary names creating sampleMap MatchedAssayExperiment constructor function now works either single MultiAssayExperiment essential components one. Renamed duplicated function replicated Added coercion functions List list ExperimentList Improve speed reshape functions previous change (wideFormat) Remove clusterOn function move Bioconductor/MultiOmicQC package GitHub duplicated deprecated, use replicated anyReplicated removed dependencies tidyr reshape2 Moved API shiny function waldronlab/MultiAssayShiny package Reduced imports (removed shinydashboard shiny) Method requirement checks classes practical using try() Deprecated methods removed: pData Deprecated class removed: RangedRaggedAssay Assay-selective subsetting implemented via list/List class subsettors","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-6-0","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.6.0","text":"Added isEmpty method ExperimentList account empty matrix Documentation improvements MultiAssayExperiment-class MultiAssayExperiment-helpers c internals improved Explicitly check DataFrame ExperimentList Fixed documentation warnings inexact links Fix subsetting order bracket method ([) Minor vignette changes Supply collapse character wideFormat column names upsetSamples munge experiment names special characters check.names = FALSE (default keeps hyphens, underscores, etc.). nameFilter functional argument allows operations substr experiment names. (@vjcitn, #231) Updates prepMultiAssay Enhancements main vignette New format NEWS section updated duplicated function now returns FALSE non-duplicated samples Improved ExperimentList constructor now handles multiple key = value entries Removed updateObject giving warning Removed old RTCGAToolbox example vignette Official manuscript citation added Improved examples (removed ExpressionSet legacy objects)","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-59","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.59","text":"rearrange now broken longFormat wideFormat functions. Helper functions now dedicated man page, see: ?'MultiAssayExperiment-helpers'","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-59","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.59","text":"subset can affect order rows (previously didn’t) rownames exclusively used create longFormat DataFrames longFormat,ExperimentList-method now returns long DataFrame Minor improvements tests","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-52","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.52","text":"reduce removed broken mergeReplicates intersectColumns Additional helper introduced: intersectRows","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-49","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.49","text":"pData deprecated favor colData Quick start vignette now available","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-49","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.49","text":"Fixed API function link Removed coercion old RangedRaggedAssay class Improved listToMap","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-44","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.44","text":"Renamed PrepMultiAssay prepMultiAssay (lower p following convention)","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-43","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.43","text":"MultiAssayExperiment quickstart guide vignette added Deprecation RangedRaggedAssay class. Use RaggedExperiment package instead. reduce function simplified mapFrom convenience argument added c,MultiAssayExperiment-method assay assays methods revised conform SummarizedExperiment standards","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-43","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.43","text":"API() now points correct web document ExperimentList constructor longer coerces GRangesList RangedRaggedAssay Documentation changes: consolidate man pages experiments, experiments<-, sampleMap, sampleMap<- removal internal getHits method, simplified helper function place prepMultiAssay helper now returns list names corresponding MultiAssayExperiment constructor function","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-37","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.37","text":"MatchedAssayExperiment subclass added matched samples assays Supply mini ACC dataset data(miniACC) Provide reference table methods package, see vignettes Merge GitHub development version","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-37","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.37","text":"ensure assay column sampleMap factor rearrange long DataFrame correctly remove support RangedRaggedAssay - deprecate drop = FALSE single column subset colData default sampleMap representation empty DataFrame colnames added combine c vignette section adding experiments existing","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-27","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.27","text":"c method implemented experiments 1:1 sample matches pData rows MultiAssayExperiment show method improved Double bracket [[ extracts single experiment (replacement also included) Internal getHits methods removed refactored subsetByRows subsetBypData available rearrange method now supports “wide” format outputs","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-27","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.27","text":"Updates HDF5 vignette examples documentation Numerous bug fixes mapToList uses efficient splitAsList function","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-17","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.17","text":"upsetSamples function implemented","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-16","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.16","text":"Implement shape argument rearrange function: wide now available","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-16","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.16","text":"Updated vignettes: DelayedMatrix & PRAD MultiAssayExperiment object","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-15","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.15","text":"disjoin method RangedRaggedAssay","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-15","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.15","text":"show method RangedRaggedAssay abbreviated. longer summarizes data assay Documentation changes reduce disjoin","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-12","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.12","text":"gather/collect function name changed rearrange clusterSex now clusterOn, works characteristic choice","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-11","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.11","text":"Renamed gather function collect","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-10","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.10","text":"Double bracket method MultiAssayExperiment available","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-9","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.9","text":"clusterSex function available clustering gender expression data","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-9","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.9","text":"Improvements documentation","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-6","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.6","text":"Added example HNSC dataset","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-6","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.6","text":"Improve documentation assay method RangedRaggedAssay Bug fixes assay method Removed method pollution Bioconductor classes assay method shows numeric character data","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-2","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.2","text":"extract method renamed gather gather allows inclusion pData columns gather method supports common classes; creates “tidy” DataFrame pData rownames, ExperimentList rownames, ExperimentList columns, assay names, optional pData columns","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-2","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.2","text":"Fix assay arguments RangedRaggedAssay method Subsetting column now arranges sampleMap proper order","code":""},{"path":[]},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"new-features-1-1-1","dir":"Changelog","previous_headings":"","what":"New features","title":"Changes in version 1.1.1","text":"extract method now available common classes - creates tidy data.frame data Example section added vignette converting data frames Bioconductor objects dimnames method added RangedRaggedAssay $ (DollarSign) method available MultiAssayExperiment access pData column metadata<- set method now available MultiAssayExperiment Improved MultiAssayExperiment constructor renamed argument “experiments” ExperimentList list input. updateObject method now available old instances MultiAssayExperiment Users invalid MultiAssayExperiments update re-serialize complete.cases method available MultiAssayExperiment class sampleMap column names renamed assay (prev. “assayname”), primary, colname (prev. “assay”) New vignete available creating MultiAssayExperiment objects TCGA data Elist class renamed ExperimentList ExperimentList constructor homonymous ExperimentList accessor now called experiments ExperimentList replacement method now experiments<- Updated vignettes reflect change names assay method RangedRaggedAssay works inner metadata columns now vignette examples available HDF5Array package Improved outline main vignette assay method available RangedRaggedAssay classes. Created obtain raw data certain classes (see ?assay,(class),-method). Subsetting non-character (#108) PrepMultiAssay helper function now available aid creating object (#122) Vignette now building (#125) Preliminary assay method RangedRaggedAssay Replacement method colnames now available RangedRaggedAssay class.","code":""},{"path":"https://github.com/waldronlab/MultiAssayExperiment/news/index.html","id":"bug-fixes-and-minor-improvements-1-1-1","dir":"Changelog","previous_headings":"","what":"Bug fixes and minor improvements","title":"Changes in version 1.1.1","text":"Documentation updated new roxygen version Improved RangedRaggedAssay rowname construction Improved show method RangedRaggedAssay class Improved MultiAssayExperiment constructor now handles stray assays, colnames, pData rownames, sampleMap rows metadata argument available MultiAssayExperiment constructor function Fix bug subsetting unmatched samples/colnames (drop = FALSE) constructor drop argument now works intended using List inherited objects proper dimnames method added MultiAssayExperiment Added informative error MultiAssayExperiment constructor Improved show method display Removed warning message ExperimentList argument provided Superfluous subset function removed sampleMap uses character vectors instead Rle Elist order consistent subsetting mapToList preserves list order","code":""}] diff --git a/sitemap.xml b/sitemap.xml index 11fd6984..16f7760f 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1,84 +1,30 @@ - - - - /404.html - - - /articles/MultiAssayExperiment.html - - - /articles/QuickStartMultiAssay.html - - - /articles/UsingHDF5Array.html - - - /articles/extras/MAE-curatedMetagenomicData.html - - - /articles/index.html - - - /authors.html - - - /index.html - - - /news/index.html - - - /reference/ExperimentList-class.html - - - /reference/ExperimentList.html - - - /reference/HDF5MultiAssayExperiment.html - - - /reference/MatchedAssayExperiment-class.html - - - /reference/MultiAssayExperiment-class.html - - - /reference/MultiAssayExperiment-helpers.html - - - /reference/MultiAssayExperiment-methods.html - - - /reference/MultiAssayExperiment-package.html - - - /reference/MultiAssayExperiment.html - - - /reference/MultiAssayExperimentToMAF.html - - - /reference/hasAssay.html - - - /reference/index.html - - - /reference/mapToList.html - - - /reference/miniACC.html - - - /reference/prepMultiAssay.html - - - /reference/reexports.html - - - /reference/subsetBy.html - - - /reference/upsetSamples.html - + +https://github.com/waldronlab/MultiAssayExperiment/404.html +https://github.com/waldronlab/MultiAssayExperiment/articles/MultiAssayExperiment.html +https://github.com/waldronlab/MultiAssayExperiment/articles/QuickStartMultiAssay.html +https://github.com/waldronlab/MultiAssayExperiment/articles/UsingHDF5Array.html +https://github.com/waldronlab/MultiAssayExperiment/articles/extras/MAE-curatedMetagenomicData.html +https://github.com/waldronlab/MultiAssayExperiment/articles/index.html +https://github.com/waldronlab/MultiAssayExperiment/authors.html +https://github.com/waldronlab/MultiAssayExperiment/index.html +https://github.com/waldronlab/MultiAssayExperiment/news/index.html +https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList-class.html +https://github.com/waldronlab/MultiAssayExperiment/reference/ExperimentList.html +https://github.com/waldronlab/MultiAssayExperiment/reference/HDF5MultiAssayExperiment.html +https://github.com/waldronlab/MultiAssayExperiment/reference/MatchedAssayExperiment-class.html +https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-class.html +https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-helpers.html +https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-methods.html +https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment-package.html +https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html +https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperimentToMAF.html +https://github.com/waldronlab/MultiAssayExperiment/reference/hasAssay.html +https://github.com/waldronlab/MultiAssayExperiment/reference/index.html +https://github.com/waldronlab/MultiAssayExperiment/reference/mapToList.html +https://github.com/waldronlab/MultiAssayExperiment/reference/miniACC.html +https://github.com/waldronlab/MultiAssayExperiment/reference/prepMultiAssay.html +https://github.com/waldronlab/MultiAssayExperiment/reference/reexports.html +https://github.com/waldronlab/MultiAssayExperiment/reference/subsetBy.html +https://github.com/waldronlab/MultiAssayExperiment/reference/upsetSamples.html +