diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index 763bbd9e..ea144684 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -117,7 +117,7 @@

Leonardo University
lcolladotor@gmail.com -

17 July 2024

+

19 July 2024

Source: vignettes/TenX_data_download.Rmd @@ -532,7 +532,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/49832febaac_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/29a341ccbf3_gencode.v32.annotation.gtf.gz" ## Import into R (takes ~1 min) gtf <- rtracklayer::import(gtf_cache) @@ -818,11 +818,11 @@

Wrapper functions= c("lowres", "hires", "detected", "aligned"), load = TRUE, reference_gtf = gtf_cache ) -#> 2024-07-17 13:57:08.168846 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-07-17 13:57:19.596362 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-07-17 13:57:19.702059 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-07-17 13:57:19.945565 rtracklayer::import: reading the reference GTF file -#> 2024-07-17 13:57:47.519521 adding gene information to the SPE object +#> 2024-07-19 16:15:59.611155 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-07-19 16:16:11.118014 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-07-19 16:16:11.222624 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-07-19 16:16:11.466511 rtracklayer::import: reading the reference GTF file +#> 2024-07-19 16:16:38.948396 adding gene information to the SPE object #> Warning: Gene IDs did not match. This typically happens when you are not using #> the same GTF file as the one that was used by SpaceRanger. For example, one #> file uses GENCODE IDs and the other one ENSEMBL IDs. read10xVisiumWrapper() @@ -830,7 +830,7 @@

Wrapper functions#> Warning: Dropping 29 out of 36601 genes for which we don't have information on #> the reference GTF file. This typically happens when you are not using the same #> GTF file as the one that was used by SpaceRanger. -#> 2024-07-17 13:57:47.776325 adding information used by spatialLIBD +#> 2024-07-19 16:16:39.203504 adding information used by spatialLIBD 
 ## Run our shiny app
 if (interactive()) {
@@ -1114,9 +1114,9 @@ 
Reproducibilitylibrary("knitr")
 knit("TenX_data_download.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-07-17 13:57:48 UTC"
+
#> [1] "2024-07-19 16:16:40 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.705 mins
+
#> Time difference of 1.684 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1128,7 +1128,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-07-17
+#>  date     2024-07-19
 #>  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -1251,7 +1251,7 @@ 
Reproducibility#>  ragg                   1.3.2     2024-05-15 [2] RSPM (R 4.4.0)
 #>  rappdirs               0.3.3     2021-01-31 [2] RSPM (R 4.4.0)
 #>  RColorBrewer           1.1-3     2022-04-03 [1] RSPM (R 4.4.0)
-#>  Rcpp                   1.0.12    2024-01-09 [2] RSPM (R 4.4.0)
+#>  Rcpp                   1.0.13    2024-07-17 [2] RSPM (R 4.4.0)
 #>  RCurl                  1.98-1.16 2024-07-11 [1] RSPM (R 4.4.0)
 #>  RefManageR           * 1.4.0     2022-09-30 [1] RSPM (R 4.4.0)
 #>  rematch2               2.1.2     2020-05-01 [2] RSPM (R 4.4.0)
@@ -1281,7 +1281,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.6    2024-07-17 [1] Bioconductor
+#>  spatialLIBD          * 1.17.6    2024-07-19 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
@@ -1299,7 +1299,7 @@ 
Reproducibility#>  viridis                0.6.5     2024-01-29 [1] RSPM (R 4.4.0)
 #>  viridisLite            0.4.2     2023-05-02 [1] RSPM (R 4.4.0)
 #>  withr                  3.0.0     2024-01-16 [2] RSPM (R 4.4.0)
-#>  xfun                   0.45      2024-06-16 [2] RSPM (R 4.4.0)
+#>  xfun                   0.46      2024-07-18 [2] RSPM (R 4.4.0)
 #>  XML                    3.99-0.17 2024-06-25 [1] RSPM (R 4.4.0)
 #>  xml2                   1.3.6     2023-12-04 [2] RSPM (R 4.4.0)
 #>  xtable                 1.8-4     2019-04-21 [2] RSPM (R 4.4.0)
diff --git a/articles/guide_to_spatial_registration.html b/articles/guide_to_spatial_registration.html
index cb254465..0ebbd284 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -101,7 +101,7 @@ 
Louise
 Development

       
                   
-            
17 July 2024

+            
19 July 2024

       
       Source: vignettes/guide_to_spatial_registration.Rmd
       
@@ -288,7 +288,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-07-17 13:54:13.294755 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:13:06.649509 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 layer_modeling_results$enrichment[1:5, 1:5]
 #>    t_stat_WM t_stat_Layer1 t_stat_Layer2 t_stat_Layer3 t_stat_Layer4
@@ -391,18 +391,18 @@ 
Get Enrichment statistics
     gene_ensembl = "gene_id",
     gene_name = "gene_name"
 )
-#> 2024-07-17 13:54:21.031386 make pseudobulk object
-#> 2024-07-17 13:54:22.727446 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-07-17 13:54:22.789323 drop lowly expressed genes
-#> 2024-07-17 13:54:22.963372 normalize expression
-#> 2024-07-17 13:54:24.427132 create model matrix
-#> 2024-07-17 13:54:24.451001 run duplicateCorrelation()
-#> 2024-07-17 13:54:37.623842 The estimated correlation is: 0.138734774807097
-#> 2024-07-17 13:54:37.626295 computing enrichment statistics
-#> 2024-07-17 13:54:38.79442 extract and reformat enrichment results
-#> 2024-07-17 13:54:38.851417 running the baseline pairwise model
-#> 2024-07-17 13:54:39.041435 computing pairwise statistics
-#> 2024-07-17 13:54:40.421524 computing F-statistics

+#> 2024-07-19 16:13:14.445509 make pseudobulk object
+#> 2024-07-19 16:13:16.139074 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-07-19 16:13:16.198582 drop lowly expressed genes
+#> 2024-07-19 16:13:16.366075 normalize expression
+#> 2024-07-19 16:13:17.871261 create model matrix
+#> 2024-07-19 16:13:17.894957 run duplicateCorrelation()
+#> 2024-07-19 16:13:31.06397 The estimated correlation is: 0.138734774807097
+#> 2024-07-19 16:13:31.06644 computing enrichment statistics
+#> 2024-07-19 16:13:32.193383 extract and reformat enrichment results
+#> 2024-07-19 16:13:32.248189 running the baseline pairwise model
+#> 2024-07-19 16:13:32.412747 computing pairwise statistics
+#> 2024-07-19 16:13:33.763915 computing F-statistics

Extract Enrichment t-statistics @@ -562,9 +562,9 @@

Reproducibilitylibrary("knitr") knit("guide_to_spatial_registration.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-07-17 13:54:41 UTC"
+
#> [1] "2024-07-19 16:13:35 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 40.965 secs
+
#> Time difference of 40.861 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -576,7 +576,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-07-17
+#>  date     2024-07-19
 #>  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -689,7 +689,7 @@ 
Reproducibility#>  ragg                   1.3.2     2024-05-15 [2] RSPM (R 4.4.0)
 #>  rappdirs               0.3.3     2021-01-31 [2] RSPM (R 4.4.0)
 #>  RColorBrewer           1.1-3     2022-04-03 [1] RSPM (R 4.4.0)
-#>  Rcpp                   1.0.12    2024-01-09 [2] RSPM (R 4.4.0)
+#>  Rcpp                   1.0.13    2024-07-17 [2] RSPM (R 4.4.0)
 #>  RCurl                  1.98-1.16 2024-07-11 [1] RSPM (R 4.4.0)
 #>  RefManageR           * 1.4.0     2022-09-30 [1] RSPM (R 4.4.0)
 #>  rematch2               2.1.2     2020-05-01 [2] RSPM (R 4.4.0)
@@ -716,7 +716,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.6    2024-07-17 [1] Bioconductor
+#>  spatialLIBD          * 1.17.6    2024-07-19 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
@@ -734,7 +734,7 @@ 
Reproducibility#>  viridis                0.6.5     2024-01-29 [1] RSPM (R 4.4.0)
 #>  viridisLite            0.4.2     2023-05-02 [1] RSPM (R 4.4.0)
 #>  withr                  3.0.0     2024-01-16 [2] RSPM (R 4.4.0)
-#>  xfun                   0.45      2024-06-16 [2] RSPM (R 4.4.0)
+#>  xfun                   0.46      2024-07-18 [2] RSPM (R 4.4.0)
 #>  XML                    3.99-0.17 2024-06-25 [1] RSPM (R 4.4.0)
 #>  xml2                   1.3.6     2023-12-04 [2] RSPM (R 4.4.0)
 #>  xtable                 1.8-4     2019-04-21 [2] RSPM (R 4.4.0)
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 847ca6a7..4d2ecf76 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -108,7 +108,7 @@ 
Leonardo
 Public Health

       
                   
-            
17 July 2024

+            
19 July 2024

       
       Source: vignettes/multi_gene_plots.Rmd
       
@@ -195,9 +195,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-07-17 13:55:06.762958 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:13:59.844049 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-07-17 13:55:07.675711 loading file /github/home/.cache/R/BiocFileCache/4987a2d0cae_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:14:00.661599 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 sig_genes <- sig_genes_extract_all(
     n = 400,
     modeling_results = modeling_results,
@@ -421,9 +421,9 @@ 
Reproducibilitylibrary("knitr")
 knit("multi_gene_plots.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-07-17 13:55:23 UTC"

+
#> [1] "2024-07-19 16:14:16 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 36.887 secs

+
#> Time difference of 36.497 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -435,7 +435,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-07-17
+#>  date     2024-07-19
 #>  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -550,7 +550,7 @@ 
Reproducibility#>  ragg                   1.3.2     2024-05-15 [2] RSPM (R 4.4.0)
 #>  rappdirs               0.3.3     2021-01-31 [2] RSPM (R 4.4.0)
 #>  RColorBrewer           1.1-3     2022-04-03 [1] RSPM (R 4.4.0)
-#>  Rcpp                   1.0.12    2024-01-09 [2] RSPM (R 4.4.0)
+#>  Rcpp                   1.0.13    2024-07-17 [2] RSPM (R 4.4.0)
 #>  RCurl                  1.98-1.16 2024-07-11 [1] RSPM (R 4.4.0)
 #>  RefManageR           * 1.4.0     2022-09-30 [1] RSPM (R 4.4.0)
 #>  rematch2               2.1.2     2020-05-01 [2] RSPM (R 4.4.0)
@@ -577,7 +577,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.6    2024-07-17 [1] Bioconductor
+#>  spatialLIBD          * 1.17.6    2024-07-19 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
@@ -595,7 +595,7 @@ 
Reproducibility#>  viridis                0.6.5     2024-01-29 [1] RSPM (R 4.4.0)
 #>  viridisLite            0.4.2     2023-05-02 [1] RSPM (R 4.4.0)
 #>  withr                  3.0.0     2024-01-16 [2] RSPM (R 4.4.0)
-#>  xfun                   0.45      2024-06-16 [2] RSPM (R 4.4.0)
+#>  xfun                   0.46      2024-07-18 [2] RSPM (R 4.4.0)
 #>  XML                    3.99-0.17 2024-06-25 [1] RSPM (R 4.4.0)
 #>  xml2                   1.3.6     2023-12-04 [2] RSPM (R 4.4.0)
 #>  xtable                 1.8-4     2019-04-21 [2] RSPM (R 4.4.0)
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index 3e707196..1cc55604 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -114,7 +114,7 @@ 
Andrew E.
 Campus

       
                   
-            
17 July 2024

+            
19 July 2024

       
       Source: vignettes/spatialLIBD.Rmd
       
@@ -414,7 +414,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-07-17 13:55:39.830372 loading file /github/home/.cache/R/BiocFileCache/4982ebeafe0_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-07-19 16:14:32.734251 loading file /github/home/.cache/R/BiocFileCache/29a3cc87240_sce_sub_for_vignette.Rdata%3Fdl%3D1
 
 ## Convert to a SpatialExperiment object
 spe <- sce_to_spe(sce)
@@ -426,9 +426,9 @@ 
Downloading the data with s
 
 ## Query ExperimentHub and download the data
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-07-17 13:55:44.107964 loading file /github/home/.cache/R/BiocFileCache/4987a2d0cae_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:14:37.037444 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-07-17 13:55:44.559624 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-07-19 16:14:37.470295 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

 
Once you have downloaded the objects, we can explore them a little
 bit

 
@@ -501,7 +501,7 @@ 
Downloading the data with s
         )
 )
 #>    user  system elapsed 
-#>   9.944   0.296  10.247
+#>   9.878   0.312  10.191
 
 ## Explore the result
 class(sig_genes)
@@ -1377,9 +1377,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-07-17 13:56:02 UTC"

+
#> [1] "2024-07-19 16:14:54 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 34.974 secs

+
#> Time difference of 34.825 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1391,7 +1391,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-07-17
+#>  date     2024-07-19
 #>  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -1506,7 +1506,7 @@ 
Reproducibility#>  ragg                   1.3.2     2024-05-15 [2] RSPM (R 4.4.0)
 #>  rappdirs               0.3.3     2021-01-31 [2] RSPM (R 4.4.0)
 #>  RColorBrewer           1.1-3     2022-04-03 [1] RSPM (R 4.4.0)
-#>  Rcpp                   1.0.12    2024-01-09 [2] RSPM (R 4.4.0)
+#>  Rcpp                   1.0.13    2024-07-17 [2] RSPM (R 4.4.0)
 #>  RCurl                  1.98-1.16 2024-07-11 [1] RSPM (R 4.4.0)
 #>  RefManageR           * 1.4.0     2022-09-30 [1] RSPM (R 4.4.0)
 #>  rematch2               2.1.2     2020-05-01 [2] RSPM (R 4.4.0)
@@ -1533,7 +1533,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.6    2024-07-17 [1] Bioconductor
+#>  spatialLIBD          * 1.17.6    2024-07-19 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
@@ -1551,7 +1551,7 @@ 
Reproducibility#>  viridis                0.6.5     2024-01-29 [1] RSPM (R 4.4.0)
 #>  viridisLite            0.4.2     2023-05-02 [1] RSPM (R 4.4.0)
 #>  withr                  3.0.0     2024-01-16 [2] RSPM (R 4.4.0)
-#>  xfun                   0.45      2024-06-16 [2] RSPM (R 4.4.0)
+#>  xfun                   0.46      2024-07-18 [2] RSPM (R 4.4.0)
 #>  XML                    3.99-0.17 2024-06-25 [1] RSPM (R 4.4.0)
 #>  xml2                   1.3.6     2023-12-04 [2] RSPM (R 4.4.0)
 #>  xtable                 1.8-4     2019-04-21 [2] RSPM (R 4.4.0)
diff --git a/pkgdown.yml b/pkgdown.yml
index f01eec79..98ccbc45 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,4 +6,4 @@ articles:
   multi_gene_plots: multi_gene_plots.html
   spatialLIBD: spatialLIBD.html
   TenX_data_download: TenX_data_download.html
-last_built: 2024-07-17T13:48Z
+last_built: 2024-07-19T16:07Z
diff --git a/reference/add_images.html b/reference/add_images.html
index db2faadf..4e9a1e4b 100644
--- a/reference/add_images.html
+++ b/reference/add_images.html
@@ -165,29 +165,29 @@ 
Examples

         image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
     ))
 }
-#> 2024-07-17 13:48:26.600477 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-07-17 13:48:41.90188 adding image for sample 151507
-#> 2024-07-17 13:48:42.538745 adding image for sample 151508
+#> 2024-07-19 16:07:22.408291 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:07:37.850974 adding image for sample 151507
+#> 2024-07-19 16:07:38.796288 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-07-17 13:48:42.539054 adding image for sample 151509
+#> 2024-07-19 16:07:38.796601 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-07-17 13:48:42.539261 adding image for sample 151510
+#> 2024-07-19 16:07:38.796806 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-07-17 13:48:42.539459 adding image for sample 151669
+#> 2024-07-19 16:07:38.797002 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-07-17 13:48:42.539652 adding image for sample 151670
+#> 2024-07-19 16:07:38.797189 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-07-17 13:48:42.539843 adding image for sample 151671
+#> 2024-07-19 16:07:38.797374 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-07-17 13:48:42.540033 adding image for sample 151672
+#> 2024-07-19 16:07:38.797563 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-07-17 13:48:42.540223 adding image for sample 151673
+#> 2024-07-19 16:07:38.79775 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-07-17 13:48:42.540414 adding image for sample 151674
+#> 2024-07-19 16:07:38.79797 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-07-17 13:48:42.540604 adding image for sample 151675
+#> 2024-07-19 16:07:38.798164 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-07-17 13:48:42.540791 adding image for sample 151676
+#> 2024-07-19 16:07:38.798351 adding image for sample 151676
 #> Warning: No image was found for sample: 151676
 #> DataFrame with 13 rows and 4 columns
 #>       sample_id    image_id   data scaleFactor
diff --git a/reference/add_key.html b/reference/add_key.html
index 220b5ded..c7e74049 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -124,7 +124,7 @@ 
Examples

     spe$key_original <- NULL
     head(spe$key)
 }
-#> 2024-07-17 13:48:44.910936 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:07:41.143035 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> [1] "151507_AAACAACGAATAGTTC-1" "151507_AAACAAGTATCTCCCA-1"
 #> [3] "151507_AAACAATCTACTAGCA-1" "151507_AAACACCAATAACTGC-1"
 #> [5] "151507_AAACAGCTTTCAGAAG-1" "151507_AAACAGGGTCTATATT-1"
diff --git a/reference/add_qc_metrics.html b/reference/add_qc_metrics.html
index 9c72a786..3e0f9ef6 100644
--- a/reference/add_qc_metrics.html
+++ b/reference/add_qc_metrics.html
@@ -144,7 +144,7 @@ 
Author

     
Examples

     
## Obtain the necessary data
 spe_pre_qc <- fetch_data("spatialDLPFC_Visium_example_subset")
-#> 2024-07-17 13:49:00.582195 loading file /github/home/.cache/R/BiocFileCache/49872dc0d45_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-07-19 16:07:56.700429 loading file /github/home/.cache/R/BiocFileCache/29a5701c74f_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
 
 ## For now, we fake out tissue spots in example data
 spe_qc <- spe_pre_qc
diff --git a/reference/annotate_registered_clusters.html b/reference/annotate_registered_clusters.html
index 50b43af5..cd1c3b07 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -137,7 +137,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-17 13:49:13.326528 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:08:09.317171 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the correlations
 cor_stats_layer <- layer_stat_cor(
diff --git a/reference/check_modeling_results.html b/reference/check_modeling_results.html
index f95254df..5d36428f 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -108,7 +108,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-17 13:49:14.441658 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:08:10.288301 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Check the object
 xx <- check_modeling_results(modeling_results)
diff --git a/reference/check_sce.html b/reference/check_sce.html
index fdc02746..b0055e79 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-07-17 13:49:15.651297 loading file /github/home/.cache/R/BiocFileCache/4982ebeafe0_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-07-19 16:08:11.376681 loading file /github/home/.cache/R/BiocFileCache/29a3cc87240_sce_sub_for_vignette.Rdata%3Fdl%3D1
 #> class: SingleCellExperiment 
 #> dim: 33538 47681 
 #> metadata(1): image
diff --git a/reference/check_sce_layer.html b/reference/check_sce_layer.html
index c926c5cf..41c7805d 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -112,7 +112,7 @@ 
Examples

 ## Obtain example data from the HumanPilot project
 ## (Maynard, Collado-Torres, et al, 2021)
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-07-17 13:49:18.090538 loading file /github/home/.cache/R/BiocFileCache/4987a2d0cae_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:08:13.754237 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Check the pseudo-bulked data
 check_sce_layer(sce_layer)
diff --git a/reference/check_spe.html b/reference/check_spe.html
index 262e37d5..a65976cf 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-07-17 13:49:19.444343 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:08:14.945897 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> class: SpatialExperiment 
 #> dim: 33538 47681 
 #> metadata(0):
diff --git a/reference/cluster_export.html b/reference/cluster_export.html
index 41dcf6be..3c1b770f 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-07-17 13:49:34.076008 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:08:29.580672 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 

diff --git a/reference/cluster_import.html b/reference/cluster_import.html
index 585bc91f..e7ddd272 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-07-17 13:49:49.230922 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:08:44.680653 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpCfl3tH/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/Rtmpa9DJI7/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpCfl3tH/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/Rtmpa9DJI7/exported_clusters/GraphBased' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 #> DataFrame with 47681 rows and 71 columns
 #>                                       key   sample_id   Cluster   sum_umi
diff --git a/reference/fetch_data.html b/reference/fetch_data.html
index 626b28ea..63fdac77 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -95,8 +95,8 @@ 
Download the Human DLPFC Visium data from LIBD

     "spatialDLPFC_Visium_SPG", "spatialDLPFC_snRNAseq",
     "Visium_SPG_AD_Visium_wholegenome_spe", "Visium_SPG_AD_Visium_targeted_spe",
     "Visium_SPG_AD_Visium_wholegenome_pseudobulk_spe",
-    "Visium_SPG_AD_Visium_wholegenome_modeling_results", "Visium_LS_spe",
-    "Visium_LS_spaceranger", "Visium_LS_ImageJ_out"),
+    "Visium_SPG_AD_Visium_wholegenome_modeling_results", "visiumStitched_brain_spe",
+    "visiumStitched_brain_spaceranger", "visiumStitched_brain_ImageJ_out"),
   destdir = tempdir(),
   eh = ExperimentHub::ExperimentHub(),
   bfc = BiocFileCache::BiocFileCache()
@@ -166,7 +166,7 @@ 
Examples

 ## Download the SingleCellExperiment object
 ## at the layer-level
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-07-17 13:50:04.599487 loading file /github/home/.cache/R/BiocFileCache/4987a2d0cae_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:00.041345 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Explore the data
 sce_layer
diff --git a/reference/frame_limits.html b/reference/frame_limits.html
index ce67964f..c4dbcacf 100644
--- a/reference/frame_limits.html
+++ b/reference/frame_limits.html
@@ -154,7 +154,7 @@ 
Examples

     ## Obtain the frame limits for one sample
     frame_limits(spe, sampleid = "151673")
 }
-#> 2024-07-17 13:50:07.106212 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:02.518133 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> $y_min
 #> [1] 64
 #> 
diff --git a/reference/gene_set_enrichment.html b/reference/gene_set_enrichment.html
index 69f114cc..fd0d8562 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -176,7 +176,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-17 13:50:21.075222 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:16.635003 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the gene set enrichment results
 asd_sfari_enrichment <- gene_set_enrichment(
diff --git a/reference/gene_set_enrichment_plot.html b/reference/gene_set_enrichment_plot.html
index ffdc11f2..a6d0ff3e 100644
--- a/reference/gene_set_enrichment_plot.html
+++ b/reference/gene_set_enrichment_plot.html
@@ -178,7 +178,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-17 13:50:22.531835 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:17.847532 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the gene set enrichment results
 asd_sfari_enrichment <- gene_set_enrichment(
diff --git a/reference/geom_spatial.html b/reference/geom_spatial.html
index 42e5c07c..6485f4fd 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-07-17 13:50:24.396394 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:19.772387 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     
diff --git a/reference/get_colors.html b/reference/get_colors.html
index dfbeb5c2..5ee0eaee 100644
--- a/reference/get_colors.html
+++ b/reference/get_colors.html
@@ -105,7 +105,7 @@ 
Examples

     

 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-07-17 13:50:39.853193 loading file /github/home/.cache/R/BiocFileCache/4987a2d0cae_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:35.050203 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Example layer colors with the corresponding names
 get_colors(libd_layer_colors, sce_layer$layer_guess)
diff --git a/reference/img_edit.html b/reference/img_edit.html
index 004b6d82..b098b04e 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -222,7 +222,7 @@ 
Examples

     x <- img_edit(spe, sampleid = "151507", brightness = 25)
     plot(x)
 }
-#> 2024-07-17 13:50:41.084926 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:36.264848 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     
diff --git a/reference/img_update.html b/reference/img_update.html
index 5d92fe1f..b091564c 100644
--- a/reference/img_update.html
+++ b/reference/img_update.html
@@ -139,7 +139,7 @@ 
Examples

     ## Reduce brightness to 25% and update the imgData()
     imgData(img_update(spe, sampleid = "151507", brightness = 25))
 }
-#> 2024-07-17 13:50:56.77859 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:51.600009 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> DataFrame with 13 rows and 4 columns
 #>       sample_id      image_id   data scaleFactor
 #>     <character>   <character> <list>   <numeric>
diff --git a/reference/img_update_all.html b/reference/img_update_all.html
index 8a0c7996..d55bdfd5 100644
--- a/reference/img_update_all.html
+++ b/reference/img_update_all.html
@@ -138,7 +138,7 @@ 
Examples

     ## update the imgData()
     imgData(img_update_all(spe, brightness = 25))
 }
-#> 2024-07-17 13:51:11.011904 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:05.774857 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> DataFrame with 24 rows and 4 columns
 #>       sample_id      image_id   data scaleFactor
 #>     <character>   <character> <list>   <numeric>
diff --git a/reference/layer_boxplot.html b/reference/layer_boxplot.html
index 302acf11..9486e30f 100644
--- a/reference/layer_boxplot.html
+++ b/reference/layer_boxplot.html
@@ -185,9 +185,9 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-17 13:51:28.503014 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:22.541804 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-07-17 13:51:29.384093 loading file /github/home/.cache/R/BiocFileCache/4987a2d0cae_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:23.419768 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Top 2 genes from the enrichment model
 sig_genes <- sig_genes_extract_all(
diff --git a/reference/layer_stat_cor.html b/reference/layer_stat_cor.html
index 208b193a..4b24508b 100644
--- a/reference/layer_stat_cor.html
+++ b/reference/layer_stat_cor.html
@@ -156,7 +156,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-17 13:51:32.756558 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:26.827106 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the correlations
 cor_stats_layer <- layer_stat_cor(
diff --git a/reference/layer_stat_cor_plot.html b/reference/layer_stat_cor_plot.html
index 7670f03a..c4838e45 100644
--- a/reference/layer_stat_cor_plot.html
+++ b/reference/layer_stat_cor_plot.html
@@ -145,7 +145,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-17 13:51:33.883339 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:27.932675 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the correlations
 cor_stats_layer <- layer_stat_cor(
diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html
index 126fabd2..57498a84 100644
--- a/reference/registration_block_cor.html
+++ b/reference/registration_block_cor.html
@@ -146,9 +146,9 @@ 
Examples

 #> 
 #> rgstr_> ## Pseudo-bulk
 #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL)
-#> 2024-07-17 13:51:37.088175 make pseudobulk object
-#> 2024-07-17 13:51:37.267087 drop lowly expressed genes
-#> 2024-07-17 13:51:37.336566 normalize expression
+#> 2024-07-19 16:10:31.154749 make pseudobulk object
+#> 2024-07-19 16:10:31.333972 drop lowly expressed genes
+#> 2024-07-19 16:10:31.402817 normalize expression
 #> 
 #> rgstr_> colData(sce_pseudo)
 #> DataFrame with 20 rows and 8 columns
@@ -180,7 +180,7 @@ 
Examples

 #> E_S                      S                      E        11
 #> 
 #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age")
-#> 2024-07-17 13:51:37.415555 create model matrix
+#> 2024-07-19 16:10:31.480569 create model matrix
 #> 
 #> rgstr_> head(registration_mod)
 #>      registration_variableG0 registration_variableG1 registration_variableG2M
@@ -198,8 +198,8 @@ 
Examples

 #> E_G0                      0 20.97006
 #> A_G1                      0 19.18719
 block_cor <- registration_block_cor(sce_pseudo, registration_mod)
-#> 2024-07-17 13:51:37.428263 run duplicateCorrelation()
-#> 2024-07-17 13:51:38.691552 The estimated correlation is: -0.0187869166526901
+#> 2024-07-19 16:10:31.493248 run duplicateCorrelation()
+#> 2024-07-19 16:10:32.781093 The estimated correlation is: -0.0187869166526901
diff --git a/reference/registration_model.html b/reference/registration_model.html index c96dc0da..b466b60b 100644 --- a/reference/registration_model.html +++ b/reference/registration_model.html @@ -148,9 +148,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-17 13:51:39.129951 make pseudobulk object -#> 2024-07-17 13:51:39.31554 drop lowly expressed genes -#> 2024-07-17 13:51:39.370617 normalize expression +#> 2024-07-19 16:10:33.217748 make pseudobulk object +#> 2024-07-19 16:10:33.403467 drop lowly expressed genes +#> 2024-07-19 16:10:33.458532 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -181,7 +181,7 @@

Examples

#> D_S S D 14 #> E_S S E 11 registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-07-17 13:51:39.447064 create model matrix +#> 2024-07-19 16:10:33.532935 create model matrix head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M #> A_G0 1 0 0 diff --git a/reference/registration_pseudobulk.html b/reference/registration_pseudobulk.html index 8722ef39..1bf72d57 100644 --- a/reference/registration_pseudobulk.html +++ b/reference/registration_pseudobulk.html @@ -159,9 +159,9 @@

Examples

## Pseudo-bulk sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-17 13:51:39.903902 make pseudobulk object -#> 2024-07-17 13:51:40.056716 drop lowly expressed genes -#> 2024-07-17 13:51:40.111023 normalize expression +#> 2024-07-19 16:10:33.990008 make pseudobulk object +#> 2024-07-19 16:10:34.145319 drop lowly expressed genes +#> 2024-07-19 16:10:34.199291 normalize expression colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns #> Mutation_Status Cell_Cycle Treatment sample_id age diff --git a/reference/registration_stats_anova.html b/reference/registration_stats_anova.html index cdc9d765..b334c950 100644 --- a/reference/registration_stats_anova.html +++ b/reference/registration_stats_anova.html @@ -180,9 +180,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-17 13:51:40.701746 make pseudobulk object -#> 2024-07-17 13:51:40.884268 drop lowly expressed genes -#> 2024-07-17 13:51:40.939518 normalize expression +#> 2024-07-19 16:10:34.787064 make pseudobulk object +#> 2024-07-19 16:10:34.965636 drop lowly expressed genes +#> 2024-07-19 16:10:35.019663 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -214,7 +214,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-07-17 13:51:41.012467 create model matrix +#> 2024-07-19 16:10:35.092247 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -233,13 +233,13 @@

Examples

#> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-07-17 13:51:41.024125 run duplicateCorrelation() -#> 2024-07-17 13:51:42.289985 The estimated correlation is: -0.0187869166526901 +#> 2024-07-19 16:10:35.104275 run duplicateCorrelation() +#> 2024-07-19 16:10:36.383178 The estimated correlation is: -0.0187869166526901 results_anova <- registration_stats_anova(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "example" ) -#> 2024-07-17 13:51:42.302664 computing F-statistics +#> 2024-07-19 16:10:36.395592 computing F-statistics head(results_anova) #> f_stat_example p_value_example fdr_example AveExpr_example ensembl gene #> 1 0.1328075 0.93918553 0.9951876 5.499488 ENSG1 gene1 @@ -254,7 +254,7 @@

Examples

block_cor = NaN, "age", gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "example" ) -#> 2024-07-17 13:51:42.365534 computing F-statistics +#> 2024-07-19 16:10:36.457284 computing F-statistics head(results_anova_nan) #> f_stat_example p_value_example fdr_example AveExpr_example ensembl gene #> 1 0.1357180 0.93736053 0.9943765 5.499488 ENSG1 gene1 @@ -276,7 +276,7 @@

Examples

covars = NULL, gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "nocovar" ) -#> 2024-07-17 13:51:42.415614 computing F-statistics +#> 2024-07-19 16:10:36.506898 computing F-statistics head(results_anova_nocovar) #> f_stat_nocovar p_value_nocovar fdr_nocovar AveExpr_nocovar ensembl gene #> 1 0.1393641 0.9351345 0.9962097 5.499488 ENSG1 gene1 diff --git a/reference/registration_stats_enrichment.html b/reference/registration_stats_enrichment.html index b97c7f9c..cd23b136 100644 --- a/reference/registration_stats_enrichment.html +++ b/reference/registration_stats_enrichment.html @@ -171,9 +171,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-17 13:51:42.992514 make pseudobulk object -#> 2024-07-17 13:51:43.146693 drop lowly expressed genes -#> 2024-07-17 13:51:43.201202 normalize expression +#> 2024-07-19 16:10:37.070904 make pseudobulk object +#> 2024-07-19 16:10:37.224566 drop lowly expressed genes +#> 2024-07-19 16:10:37.278291 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -205,7 +205,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-07-17 13:51:43.274381 create model matrix +#> 2024-07-19 16:10:37.35073 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -224,14 +224,14 @@

Examples

#> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-07-17 13:51:43.285637 run duplicateCorrelation() -#> 2024-07-17 13:51:44.583617 The estimated correlation is: -0.0187869166526901 +#> 2024-07-19 16:10:37.36194 run duplicateCorrelation() +#> 2024-07-19 16:10:38.660422 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-07-17 13:51:44.587859 computing enrichment statistics -#> 2024-07-17 13:51:44.705956 extract and reformat enrichment results +#> 2024-07-19 16:10:38.664043 computing enrichment statistics +#> 2024-07-19 16:10:38.780433 extract and reformat enrichment results head(results_enrichment) #> t_stat_G0 t_stat_G1 t_stat_G2M t_stat_S p_value_G0 p_value_G1 #> Gene_0001 0.1482017 0.5610669 -0.3612235 -0.3458508 0.88374480 0.58130631 @@ -260,8 +260,8 @@

Examples

block_cor = NaN, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-07-17 13:51:44.739083 computing enrichment statistics -#> 2024-07-17 13:51:44.842281 extract and reformat enrichment results +#> 2024-07-19 16:10:38.812893 computing enrichment statistics +#> 2024-07-19 16:10:38.915076 extract and reformat enrichment results head(results_enrichment_nan) #> t_stat_G0 t_stat_G1 t_stat_G2M t_stat_S p_value_G0 p_value_G1 #> Gene_0001 0.1497747 0.56711100 -0.3650801 -0.3495404 0.88252049 0.57727506 diff --git a/reference/registration_stats_pairwise.html b/reference/registration_stats_pairwise.html index 03bff131..916013c2 100644 --- a/reference/registration_stats_pairwise.html +++ b/reference/registration_stats_pairwise.html @@ -173,9 +173,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-17 13:51:45.303165 make pseudobulk object -#> 2024-07-17 13:51:45.456984 drop lowly expressed genes -#> 2024-07-17 13:51:45.511196 normalize expression +#> 2024-07-19 16:10:39.376626 make pseudobulk object +#> 2024-07-19 16:10:39.529488 drop lowly expressed genes +#> 2024-07-19 16:10:39.583602 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -207,7 +207,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-07-17 13:51:45.621594 create model matrix +#> 2024-07-19 16:10:39.682072 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -226,14 +226,14 @@

Examples

#> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-07-17 13:51:45.632849 run duplicateCorrelation() -#> 2024-07-17 13:51:46.88774 The estimated correlation is: -0.0187869166526901 +#> 2024-07-19 16:10:39.693149 run duplicateCorrelation() +#> 2024-07-19 16:10:40.967476 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-07-17 13:51:46.889688 running the baseline pairwise model -#> 2024-07-17 13:51:46.906431 computing pairwise statistics +#> 2024-07-19 16:10:40.969445 running the baseline pairwise model +#> 2024-07-19 16:10:40.985843 computing pairwise statistics head(results_pairwise) #> t_stat_G0-G1 t_stat_G0-G2M t_stat_G0-S t_stat_G1-G2M t_stat_G1-S #> Gene_0001 -0.2393683 0.29771391 0.28880637 0.5370822 0.5281747 @@ -277,8 +277,8 @@

Examples

block_cor = NaN, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-07-17 13:51:46.971696 running the baseline pairwise model -#> 2024-07-17 13:51:46.989106 computing pairwise statistics +#> 2024-07-19 16:10:41.050011 running the baseline pairwise model +#> 2024-07-19 16:10:41.067112 computing pairwise statistics head(results_pairwise_nan) #> t_stat_G0-G1 t_stat_G0-G2M t_stat_G0-S t_stat_G1-G2M t_stat_G1-S #> Gene_0001 -0.2419770 0.30095840 0.29195379 0.5429354 0.5339308 diff --git a/reference/registration_wrapper.html b/reference/registration_wrapper.html index a04252d2..800bb058 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -200,18 +200,18 @@

Examples

sce, "Cell_Cycle", "sample_id", c("age"), "ensembl", "gene_name", "wrapper" ) -#> 2024-07-17 13:51:47.541862 make pseudobulk object -#> 2024-07-17 13:51:47.707925 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-07-17 13:51:47.729853 drop lowly expressed genes -#> 2024-07-17 13:51:47.785167 normalize expression -#> 2024-07-17 13:51:47.8429 create model matrix -#> 2024-07-17 13:51:47.853499 run duplicateCorrelation() -#> 2024-07-17 13:51:50.267571 The estimated correlation is: -0.0783081238514532 -#> 2024-07-17 13:51:50.269845 computing enrichment statistics -#> 2024-07-17 13:51:50.386595 extract and reformat enrichment results -#> 2024-07-17 13:51:50.412505 running the baseline pairwise model -#> 2024-07-17 13:51:50.430847 computing pairwise statistics -#> 2024-07-17 13:51:50.505218 computing F-statistics +#> 2024-07-19 16:10:41.620107 make pseudobulk object +#> 2024-07-19 16:10:41.774995 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-07-19 16:10:41.796912 drop lowly expressed genes +#> 2024-07-19 16:10:41.852361 normalize expression +#> 2024-07-19 16:10:41.910191 create model matrix +#> 2024-07-19 16:10:41.92079 run duplicateCorrelation() +#> 2024-07-19 16:10:44.324436 The estimated correlation is: -0.0783081238514532 +#> 2024-07-19 16:10:44.326643 computing enrichment statistics +#> 2024-07-19 16:10:44.442721 extract and reformat enrichment results +#> 2024-07-19 16:10:44.468326 running the baseline pairwise model +#> 2024-07-19 16:10:44.486197 computing pairwise statistics +#> 2024-07-19 16:10:44.560061 computing F-statistics diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index e0797fb6..e1b882a6 100644 --- a/reference/sce_to_spe.html +++ b/reference/sce_to_spe.html @@ -127,7 +127,7 @@

Examples

## Transform it to a SpatialExperiment object spe <- sce_to_spe(sce) } -#> 2024-07-17 13:51:52.727073 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:10:46.443173 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/sig_genes_extract.html b/reference/sig_genes_extract.html index 4c448c85..972ca003 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -156,9 +156,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-07-17 13:52:05.714888 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-07-19 16:10:59.439626 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-07-17 13:52:06.659035 loading file /github/home/.cache/R/BiocFileCache/4987a2d0cae_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:11:00.380846 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## anova top 10 genes sig_genes_extract( diff --git a/reference/sig_genes_extract_all.html b/reference/sig_genes_extract_all.html index 4a42f61e..c3b5c867 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -128,9 +128,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-07-17 13:52:10.311903 loading file /github/home/.cache/R/BiocFileCache/4981423d30a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-07-19 16:11:04.11671 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-07-17 13:52:11.371345 loading file /github/home/.cache/R/BiocFileCache/4987a2d0cae_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:11:05.078106 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## top 10 genes for all models sig_genes_extract_all( diff --git a/reference/vis_clus.html b/reference/vis_clus.html index 29b47fed..93edef26 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -242,7 +242,7 @@

Examples

) print(p4) } -#> 2024-07-17 13:52:14.053539 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:11:07.56844 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_clus_p.html b/reference/vis_clus_p.html index 1e416396..f7a53154 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-07-17 13:52:33.265544 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:11:26.792648 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index f0e49f68..0af066ac 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -341,7 +341,7 @@

Examples

) print(p8) } -#> 2024-07-17 13:52:48.10019 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:11:41.686731 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene_p.html b/reference/vis_gene_p.html index 4f32d6a8..b54dba4c 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -215,7 +215,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-07-17 13:53:14.003193 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:12:07.80877 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_grid_clus.html b/reference/vis_grid_clus.html index a1aec073..8070a36e 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -237,7 +237,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-07-17 13:53:29.053452 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:12:22.629178 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_grid_gene.html b/reference/vis_grid_gene.html index 7f5c56b0..01a73127 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -256,7 +256,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-07-17 13:53:45.486537 loading file /github/home/.cache/R/BiocFileCache/f66381e3f71_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:12:38.901329 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1