diff --git a/404.html b/404.html index 826bc3a..c7d4a7f 100644 --- a/404.html +++ b/404.html @@ -6,6 +6,12 @@ Page not found (404) • visiumStitched + + + + + + @@ -93,7 +99,7 @@

Page not found (404)

-

Site built with pkgdown 2.1.0.9000.

+

Site built with pkgdown 2.1.0.

diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 07748f4..534cd31 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -1,5 +1,5 @@ -NA • visiumStitchedNA • visiumStitched @@ -79,7 +79,7 @@

NA

-

Site built with pkgdown 2.1.0.9000.

+

Site built with pkgdown 2.1.0.

diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 323f6b1..19a99bb 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -1,5 +1,5 @@ -Contributing to visiumStitched • visiumStitchedContributing to visiumStitched • visiumStitched @@ -95,7 +95,7 @@

Code of Conduct
-

Site built with pkgdown 2.1.0.9000.

+

Site built with pkgdown 2.1.0.

diff --git a/SUPPORT.html b/SUPPORT.html index 0b78be5..ea8d290 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -1,5 +1,5 @@ -Getting help with visiumStitched • visiumStitchedGetting help with visiumStitched • visiumStitched @@ -93,7 +93,7 @@

What happens next? -

Site built with pkgdown 2.1.0.9000.

+

Site built with pkgdown 2.1.0.

diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png new file mode 100644 index 0000000..bd3b56d Binary files /dev/null and b/apple-touch-icon-120x120.png differ diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png new file mode 100644 index 0000000..dcec3de Binary files /dev/null and b/apple-touch-icon-152x152.png differ diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png new file mode 100644 index 0000000..9854ac1 Binary files /dev/null and b/apple-touch-icon-180x180.png differ diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png new file mode 100644 index 0000000..3414a92 Binary files /dev/null and b/apple-touch-icon-60x60.png differ diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png new file mode 100644 index 0000000..bd8e1ee Binary files /dev/null and b/apple-touch-icon-76x76.png differ diff --git a/apple-touch-icon.png b/apple-touch-icon.png new file mode 100644 index 0000000..937616d Binary files /dev/null and b/apple-touch-icon.png differ diff --git a/articles/index.html b/articles/index.html index 39fed1c..d86ff38 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,5 +1,5 @@ -Articles • visiumStitchedArticles • visiumStitched @@ -65,7 +65,7 @@

All vignettes

-

Site built with pkgdown 2.1.0.9000.

+

Site built with pkgdown 2.1.0.

diff --git a/articles/visiumStitched.html b/articles/visiumStitched.html index 763890a..9366773 100644 --- a/articles/visiumStitched.html +++ b/articles/visiumStitched.html @@ -6,6 +6,12 @@ Introduction to visiumStitched • visiumStitched + + + + + + @@ -87,7 +93,7 @@

Leonardo

26 July 2024

- Source: vignettes/visiumStitched.Rmd + Source: vignettes/visiumStitched.Rmd @@ -100,7 +106,7 @@

Basics

Install visiumStitched

-

visiumStitched +

visiumStitched is a R package available from GitHub. It can be installed with the following commands in your R session:

@@ -114,7 +120,7 @@

Install visiumStitched

Citing visiumStitched

-

We hope that visiumStitched +

We hope that visiumStitched will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

@@ -130,8 +136,8 @@ 
Citing visiumStitched#>   package version 0.99.0,
 #>   <http://www.bioconductor.org/packages/visiumStitched>.
 #> 
-#>   Eagles NJ, Bach S, Tippani M, Du Y, Hyde TM, Page SC, Martinowich K,
-#>   Collado-Torres L (2024). "visiumStitched." _bioRxiv_.
+#>   Eagles NJ, Bach S, Tippani M, Du Y, Miller RA, Hyde TM, Page SC,
+#>   Martinowich K, Collado-Torres L (2024). "visiumStitched." _bioRxiv_.
 #>   doi:10.1101/TODO <https://doi.org/10.1101/TODO>,
 #>   <https://www.biorxiv.org/content/10.1101/TODO>.
 #> 
@@ -187,7 +193,7 @@ 
Preparing Experiment Informationsr_dir <- tempdir()
 temp <- unzip(spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir)
-#> 2024-07-26 18:57:50.070552 loading file /github/home/.cache/R/BiocFileCache/2ab3be94b44_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 17:09:27.963631 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d1b42d2d8_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -195,11 +201,11 @@ 
Preparing Experiment Information## Sample_info with paths to SpaceRanger output directories
 sample_info
 #> # A tibble: 3 × 3
-#>   group  capture_area  spaceranger_dir                           
-#>   <chr>  <chr>         <chr>                                     
-#> 1 Br2719 V13B23-283_A1 /tmp/RtmpyEdeBe/V13B23-283_A1/outs/spatial
-#> 2 Br2719 V13B23-283_C1 /tmp/RtmpyEdeBe/V13B23-283_C1/outs/spatial
-#> 3 Br2719 V13B23-283_D1 /tmp/RtmpyEdeBe/V13B23-283_D1/outs/spatial
+#> group capture_area spaceranger_dir +#> <chr> <chr> <chr> +#> 1 Br2719 V13B23-283_A1 /var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//RtmpoU… +#> 2 Br2719 V13B23-283_C1 /var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//RtmpoU… +#> 3 Br2719 V13B23-283_D1 /var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//RtmpoU…

Preparing Inputs to Fiji @@ -228,9 +234,9 @@

Preparing Inputs to Fiji#> # A tibble: 3 × 5 #> group capture_area spaceranger_dir intra_group_scalar group_hires_scalef #> <chr> <chr> <chr> <dbl> <dbl> -#> 1 Br2719 V13B23-283_A1 /tmp/RtmpyEdeBe/V1… 1.00 0.0825 -#> 2 Br2719 V13B23-283_C1 /tmp/RtmpyEdeBe/V1… 1.00 0.0825 -#> 3 Br2719 V13B23-283_D1 /tmp/RtmpyEdeBe/V1… 1 0.0825

+#> 1 Br2719 V13B23-283_A1 /var/folders/_2/hq… 1.00 0.0825 +#> 2 Br2719 V13B23-283_C1 /var/folders/_2/hq… 1.00 0.0825 +#> 3 Br2719 V13B23-283_D1 /var/folders/_2/hq… 1 0.0825

Building a SpatialExperiment @@ -258,7 +264,7 @@

Creating Group-Level Samples
 fiji_dir <- tempdir()
 temp <- unzip(fetch_data("visiumStitched_brain_Fiji_out"), exdir = fiji_dir)
-#> 2024-07-26 18:58:05.767483 loading file /github/home/.cache/R/BiocFileCache/2ab78c3d33f_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 17:09:36.25476 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d4e4f1593_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
 sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
 sample_info$fiji_image_path <- temp[grep("png$", temp)]

We now have every column present in sample_info that @@ -269,9 +275,9 @@

Creating Group-Level Samples#> # A tibble: 3 × 7 #> group capture_area spaceranger_dir intra_group_scalar group_hires_scalef #> <chr> <chr> <chr> <dbl> <dbl> -#> 1 Br2719 V13B23-283_A1 /tmp/RtmpyEdeBe/V1… 1.00 0.0825 -#> 2 Br2719 V13B23-283_C1 /tmp/RtmpyEdeBe/V1… 1.00 0.0825 -#> 3 Br2719 V13B23-283_D1 /tmp/RtmpyEdeBe/V1… 1 0.0825 +#> 1 Br2719 V13B23-283_A1 /var/folders/_2/hq… 1.00 0.0825 +#> 2 Br2719 V13B23-283_C1 /var/folders/_2/hq… 1.00 0.0825 +#> 3 Br2719 V13B23-283_D1 /var/folders/_2/hq… 1 0.0825 #> # ℹ 2 more variables: fiji_xml_path <chr>, fiji_image_path <chr>

Before building the SpatialExperiment, the idea is to create a directory structure very similar to Spaceranger’s @@ -294,10 +300,10 @@

Creating Group-Level Samples## the standard directory structure from SpaceRanger (10x Genomics) spe_input_dir <- tempdir() prep_fiji_coords(sample_info, out_dir = spe_input_dir) -#> [1] "/tmp/RtmpyEdeBe/Br2719/tissue_positions.csv" +#> [1] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//RtmpoUxRYN/Br2719/tissue_positions.csv" prep_fiji_image(sample_info, out_dir = spe_input_dir) -#> [1] "/tmp/RtmpyEdeBe/Br2719/tissue_lowres_image.png" -#> [2] "/tmp/RtmpyEdeBe/Br2719/scalefactors_json.json" +#> [1] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//RtmpoUxRYN/Br2719/tissue_lowres_image.png" +#> [2] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//RtmpoUxRYN/Br2719/scalefactors_json.json"

Constructing the Object @@ -338,11 +344,11 @@

Constructing the Object coords_dir = spe_input_dir, reference_gtf = gtf_cache ) #> Building SpatialExperiment using capture area as sample ID -#> 2024-07-26 18:58:09.008542 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-07-26 18:58:16.013081 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-07-26 18:58:16.433992 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-07-26 18:58:16.796743 rtracklayer::import: reading the reference GTF file -#> 2024-07-26 18:58:48.916211 adding gene information to the SPE object +#> 2024-07-26 17:09:38.152721 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-07-26 17:09:42.954806 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-07-26 17:09:43.308814 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-07-26 17:09:43.621759 rtracklayer::import: reading the reference GTF file +#> 2024-07-26 17:10:12.679884 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() @@ -350,7 +356,7 @@

Constructing the Object#> Warning: Dropping 2226 out of 38606 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. -#> 2024-07-26 18:58:49.149939 adding information used by spatialLIBD +#> 2024-07-26 17:10:12.868458 adding information used by spatialLIBD #> Overwriting imgData(spe) with merged images (one per group) ## The images in this example data have to be mirrored across the horizontal axis. @@ -512,7 +518,7 @@

A note on normalization
 ## Grab SpatialExperiment with normalized counts
 spe_norm <- fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 18:58:58.602928 loading file /github/home/.cache/R/BiocFileCache/2ab2fc23300_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 17:10:18.543829 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/154352e7328f0_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
 
 wm_genes_ens <- rownames(spe_norm)[
     match(c("MBP", "GFAP", "PLP1", "AQP4"), rowData(spe_norm)$gene_name)
@@ -607,22 +613,22 @@ 
Conclusion
 
Reproducibility
 

-
The visiumStitched
+
The visiumStitched
 package (Eagles and Collado-Torres, 2024) was made possible thanks
 to:

 
-
This package was developed using biocthis.

+
This package was developed using biocthis.

 
Code for creating the vignette

 
 ## Create the vignette
@@ -689,265 +695,264 @@ 
Reproducibilitylibrary("knitr")
 knit("visiumStitched.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-07-26 18:59:06 UTC"

+
#> [1] "2024-07-26 17:10:22 EDT"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 1.52 mins

+
#> Time difference of 1.069 mins

 
R session information.

 
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-#>  system   x86_64, linux-gnu
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+#>  system   aarch64, darwin20
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 #>  language en
 #>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
-#>  tz       UTC
+#>  tz       America/New_York
 #>  date     2024-07-26
-#>  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
+#>  pandoc   3.2 @ /opt/homebrew/bin/ (via rmarkdown)
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Bibliography

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This vignette was generated using BiocStyle +

This vignette was generated using BiocStyle (Oleś, 2024) with knitr (Xie, 2024) and rmarkdown (Allaire, Xie, Dervieux et al., 2024) running behind the scenes.

@@ -962,14 +967,14 @@

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Bibliography[9] A. Oleś. BiocStyle: Standard styles for vignettes and other -Bioconductor documents. R package version 2.33.1. 2024. DOI: +Bioconductor documents. R package version 2.32.1. 2024. DOI: 10.18129/B9.bioc.BiocStyle. URL: https://bioconductor.org/packages/BiocStyle. @@ -1024,7 +1029,7 @@

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Bibliography

-

Site built with pkgdown 2.1.0.9000.

+

Site built with pkgdown 2.1.0.

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Authors and Citation

Citation

- Source: inst/CITATION + Source: inst/CITATION
@@ -80,14 +80,14 @@

Citation

note = {https://github.com/LieberInstitute/visiumStitched/visiumStitched - R package version 0.99.0}, doi = {10.18129/B9.bioc.visiumStitched}, } -

Eagles NJ, Bach S, Tippani M, Du Y, Hyde TM, Page SC, Martinowich K, Collado-Torres L (2024). +

Eagles NJ, Bach S, Tippani M, Du Y, Miller RA, Hyde TM, Page SC, Martinowich K, Collado-Torres L (2024). “visiumStitched.” bioRxiv. doi:10.1101/TODO, https://www.biorxiv.org/content/10.1101/TODO. 

@Article{,
   title = {visiumStitched},
-  author = {Nicholas J. Eagles and Svitlana Bach and Madhavi Tippani and Yufeng Du and Thomas M. Hyde and Stephanie C. Page and Keri Martinowich and Leonardo Collado-Torres},
+  author = {Nicholas J. Eagles and Svitlana Bach and Madhavi Tippani and Yufeng Du and Ryan A. Miller and Thomas M. Hyde and Stephanie C. Page and Keri Martinowich and Leonardo Collado-Torres},
   year = {2024},
   journal = {bioRxiv},
   doi = {10.1101/TODO},
@@ -105,7 +105,7 @@ 
Citation

 
 
 

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 Enable downstream analysis of Visium capture areas stitched together with Fiji • visiumStitched
+
+
+
+
+
+
 
 
 
@@ -87,7 +93,7 @@ 
Example data processed with
 
 ## Download the spot-level data, which is a SpatialExperiment object
 spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 14:06:21.739878 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/154352e7328f0_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 17:05:30.544877 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/154352e7328f0_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
 
 ## Explore the stitched data
 spe
@@ -150,8 +156,8 @@ 
Citation#>     doi = {10.18129/B9.bioc.visiumStitched},
 #>   }
 #> 
-#>   Eagles NJ, Bach S, Tippani M, Du Y, Hyde TM, Page SC, Martinowich K,
-#>   Collado-Torres L (2024). "visiumStitched." _bioRxiv_.
+#>   Eagles NJ, Bach S, Tippani M, Du Y, Miller RA, Hyde TM, Page SC,
+#>   Martinowich K, Collado-Torres L (2024). "visiumStitched." _bioRxiv_.
 #>   doi:10.1101/TODO <https://doi.org/10.1101/TODO>,
 #>   <https://www.biorxiv.org/content/10.1101/TODO>.
 #> 
@@ -159,7 +165,7 @@ 
Citation#> 
 #>   @Article{,
 #>     title = {visiumStitched},
-#>     author = {Nicholas J. Eagles and Svitlana Bach and Madhavi Tippani and Yufeng Du and Thomas M. Hyde and Stephanie C. Page and Keri Martinowich and Leonardo Collado-Torres},
+#>     author = {Nicholas J. Eagles and Svitlana Bach and Madhavi Tippani and Yufeng Du and Ryan A. Miller and Thomas M. Hyde and Stephanie C. Page and Keri Martinowich and Leonardo Collado-Torres},
 #>     year = {2024},
 #>     journal = {bioRxiv},
 #>     doi = {10.1101/TODO},
@@ -257,7 +263,7 @@ 
Dev status

 
 

   

-
Site built with pkgdown 2.1.0.9000.

+
Site built with pkgdown 2.1.0.

 

 
       
diff --git a/news/index.html b/news/index.html
index d4460e3..3ac6840 100644
--- a/news/index.html
+++ b/news/index.html
@@ -1,5 +1,5 @@
 
-Changelog • visiumStitchedChangelog • visiumStitched
@@ -47,7 +47,7 @@
   

     

       
Changelog 

-      Source: NEWS.md
+      Source: NEWS.md
     

 
     

@@ -69,7 +69,7 @@ 
visiumSt
 

 
 

-  
Site built with pkgdown 2.1.0.9000.

+  
Site built with pkgdown 2.1.0.

 

 
       

diff --git a/pkgdown.yml b/pkgdown.yml
index e9e58c9..eb028e3 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,6 +1,6 @@
 pandoc: '3.2'
-pkgdown: 2.1.0.9000
-pkgdown_sha: 6f01c9267a1cee263216cec38eea10017d751dd8
+pkgdown: 2.1.0
+pkgdown_sha: ~
 articles:
   visiumStitched: visiumStitched.html
-last_built: 2024-07-26T18:55Z
+last_built: 2024-07-26T21:07Z
diff --git a/reference/Rplot002.png b/reference/Rplot002.png
deleted file mode 100644
index 8c9ad92..0000000
Binary files a/reference/Rplot002.png and /dev/null differ
diff --git a/reference/add_array_coords.html b/reference/add_array_coords.html
index 6c65800..5faf4fb 100644
--- a/reference/add_array_coords.html
+++ b/reference/add_array_coords.html
@@ -1,5 +1,5 @@
 
-Add transformed array and pixel coordinates to a SpatialExperiment — add_array_coords • visiumStitchedAdd transformed array and pixel coordinates to a SpatialExperiment — add_array_coords • visiumStitched
     

     
Add transformed array and pixel coordinates to a SpatialExperiment

-    Source: R/add_array_coords.R
+    Source: R/add_array_coords.R
     
     

 
@@ -125,7 +125,8 @@ 
Author

     

     
Examples

     
spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 18:55:26.187132 loading file /github/home/.cache/R/BiocFileCache/2ab2fc23300_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:07:42.407375 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/154352e7328f0_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
 
 ########################################################################
 #   Prepare sample_info
@@ -141,7 +142,8 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-26 18:55:30.907875 loading file /github/home/.cache/R/BiocFileCache/2ab3be94b44_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:07:45.14042 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d1b42d2d8_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -152,7 +154,8 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-26 18:55:33.641794 loading file /github/home/.cache/R/BiocFileCache/2ab78c3d33f_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:07:46.685482 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d4e4f1593_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
 sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
 sample_info$fiji_image_path <- temp[grep("png$", temp)]
 
@@ -162,10 +165,10 @@ 
Examples

 ## Preparing Fiji coordinates and images for build_spe()
 spe_input_dir <- tempdir()
 prep_fiji_coords(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/RtmpZpoicf/Br2719/tissue_positions.csv"
+#> [1] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//Rtmp355bXj/Br2719/tissue_positions.csv"
 prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/RtmpZpoicf/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpZpoicf/Br2719/scalefactors_json.json" 
+#> [1] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//Rtmp355bXj/Br2719/tissue_lowres_image.png"
+#> [2] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//Rtmp355bXj/Br2719/scalefactors_json.json" 
 
 ########################################################################
 #   Add array coordinates
@@ -210,7 +213,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.9000.

+  
Site built with pkgdown 2.1.0.

 

 
       

diff --git a/reference/add_overlap_info.html b/reference/add_overlap_info.html
index 7ae5028..e0153c4 100644
--- a/reference/add_overlap_info.html
+++ b/reference/add_overlap_info.html
@@ -1,5 +1,5 @@
 
-Add info about how spots overlap among capture areas — add_overlap_info • visiumStitchedAdd info about how spots overlap among capture areas — add_overlap_info • visiumStitchedBuild stitched SpatialExperiment — build_spe • visiumStitched
     

     
Build stitched SpatialExperiment

-    Source: R/build_spe.R
+    Source: R/build_spe.R
     
     

 
@@ -149,7 +149,8 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-26 18:55:52.653221 loading file /github/home/.cache/R/BiocFileCache/2ab3be94b44_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:07:57.930249 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d1b42d2d8_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -160,7 +161,8 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-26 18:55:55.557503 loading file /github/home/.cache/R/BiocFileCache/2ab78c3d33f_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:08:03.306954 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d4e4f1593_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
 sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
 sample_info$fiji_image_path <- temp[grep("png$", temp)]
 
@@ -170,10 +172,10 @@ 
Examples

 ## Preparing Fiji coordinates and images for build_spe()
 spe_input_dir <- tempdir()
 prep_fiji_coords(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/RtmpZpoicf/Br2719/tissue_positions.csv"
+#> [1] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//Rtmp355bXj/Br2719/tissue_positions.csv"
 prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/RtmpZpoicf/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpZpoicf/Br2719/scalefactors_json.json" 
+#> [1] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//Rtmp355bXj/Br2719/tissue_lowres_image.png"
+#> [2] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//Rtmp355bXj/Br2719/scalefactors_json.json" 
 
 ########################################################################
 #   Build the SpatialExperiment
@@ -199,14 +201,14 @@ 
Examples

     coords_dir = spe_input_dir, reference_gtf = gtf_cache
 )
 #> Building SpatialExperiment using capture area as sample ID
-#> 2024-07-26 18:56:01.509769 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
-#> 2024-07-26 18:56:07.527648 read10xVisiumAnalysis: reading analysis output from SpaceRanger
-#> 2024-07-26 18:56:07.944782 add10xVisiumAnalysis: adding analysis output from SpaceRanger
-#> 2024-07-26 18:56:08.274091 rtracklayer::import: reading the reference GTF file
-#> 2024-07-26 18:56:37.226862 adding gene information to the SPE object
+#> 2024-07-26 17:08:07.306364 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
+#> 2024-07-26 17:08:11.955257 read10xVisiumAnalysis: reading analysis output from SpaceRanger
+#> 2024-07-26 17:08:12.337616 add10xVisiumAnalysis: adding analysis output from SpaceRanger
+#> 2024-07-26 17:08:12.572514 rtracklayer::import: reading the reference GTF file
+#> 2024-07-26 17:08:39.877082 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() will try to convert them to ENSEMBL IDs.
 #> Warning: Dropping 2226 out of 38606 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.
-#> 2024-07-26 18:56:37.467851 adding information used by spatialLIBD
+#> 2024-07-26 17:08:40.072748 adding information used by spatialLIBD
 #> Overwriting imgData(spe) with merged images (one per group)
 
 ## Let's explore the stitched SpatialExperiment object
@@ -242,7 +244,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.1.0.9000.

+  
Site built with pkgdown 2.1.0.

 

 
       
diff --git a/reference/dot-clean_round.html b/reference/dot-clean_round.html
index 9934156..9baceef 100644
--- a/reference/dot-clean_round.html
+++ b/reference/dot-clean_round.html
@@ -1,5 +1,5 @@
 
-Round to the nearest integer, always rounding up at 0.5 — .clean_round • visiumStitchedRound to the nearest integer, always rounding up at 0.5 — .clean_round • visiumStitchedFit spots to a new Visium-like array — .fit_to_array • visiumStitchedFit spots to a new Visium-like array — .fit_to_array • visiumStitched
     

     
Fit spots to a new Visium-like array

-    Source: R/array_coord_utils.R
+    Source: R/array_coord_utils.R
     
     

 
@@ -111,7 +111,7 @@ 
Author

 
 
 

-  
Site built with pkgdown 2.1.0.9000.

+  
Site built with pkgdown 2.1.0.

 

 
       
diff --git a/reference/dot-refine_fit.html b/reference/dot-refine_fit.html
index 1451f4b..0db8fe2 100644
--- a/reference/dot-refine_fit.html
+++ b/reference/dot-refine_fit.html
@@ -1,5 +1,5 @@
 
-Return array coordinates fit to nearest spot with associated error — .refine_fit • visiumStitchedReturn array coordinates fit to nearest spot with associated error — .refine_fit • visiumStitched
     

     
Return array coordinates fit to nearest spot with associated error

-    Source: R/array_coord_utils.R
+    Source: R/array_coord_utils.R
     
     

 
@@ -115,7 +115,7 @@ 
Author

 
 
 

-  
Site built with pkgdown 2.1.0.9000.

+  
Site built with pkgdown 2.1.0.

 

 
       
diff --git a/reference/dot-validate_array.html b/reference/dot-validate_array.html
index 1fe1b05..be99e2d 100644
--- a/reference/dot-validate_array.html
+++ b/reference/dot-validate_array.html
@@ -1,5 +1,5 @@
 
-Check if coordinates are Visium-like — .validate_array • visiumStitchedCheck if coordinates are Visium-like — .validate_array • visiumStitchedPackage index • visiumStitchedPackage index • visiumStitched
@@ -94,7 +94,7 @@ 
All functions 
 
 

-  
Site built with pkgdown 2.1.0.9000.

+  
Site built with pkgdown 2.1.0.

 

 
       
diff --git a/reference/prep_fiji_coords.html b/reference/prep_fiji_coords.html
index bd2cba5..46a97e0 100644
--- a/reference/prep_fiji_coords.html
+++ b/reference/prep_fiji_coords.html
@@ -1,5 +1,5 @@
 
-Apply transform info from Fiji XML output — prep_fiji_coords • visiumStitchedApply transform info from Fiji XML output — prep_fiji_coords • visiumStitched
     

     
Apply transform info from Fiji XML output

-    Source: R/prep_fiji_coords.R
+    Source: R/prep_fiji_coords.R
     
     

 
@@ -111,7 +111,8 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-26 18:56:41.706106 loading file /github/home/.cache/R/BiocFileCache/2ab3be94b44_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:08:42.929996 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d1b42d2d8_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -122,7 +123,8 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-26 18:56:44.524254 loading file /github/home/.cache/R/BiocFileCache/2ab78c3d33f_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:08:44.618946 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d4e4f1593_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
 sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
 sample_info$fiji_image_path <- temp[grep("png$", temp)]
 
@@ -132,7 +134,7 @@ 
Examples

 spe_input_dir <- tempdir()
 out_file <- prep_fiji_coords(sample_info, out_dir = spe_input_dir)
 out_file
-#> [1] "/tmp/RtmpZpoicf/Br2719/tissue_positions.csv"
+#> [1] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//Rtmp355bXj/Br2719/tissue_positions.csv"
 
 #    A file of spatial coordinates for the stitched Br2719 was produced
 readr::read_csv(out_file)
@@ -172,7 +174,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.1.0.9000.

+  
Site built with pkgdown 2.1.0.

 

 
       
diff --git a/reference/prep_fiji_image-1.png b/reference/prep_fiji_image-1.png
index 389c120..064c849 100644
Binary files a/reference/prep_fiji_image-1.png and b/reference/prep_fiji_image-1.png differ
diff --git a/reference/prep_fiji_image.html b/reference/prep_fiji_image.html
index 792aad8..429228e 100644
--- a/reference/prep_fiji_image.html
+++ b/reference/prep_fiji_image.html
@@ -1,5 +1,5 @@
 
-Create low-res images and scale factors from high-res Fiji output images — prep_fiji_image • visiumStitchedCreate low-res images and scale factors from high-res Fiji output images — prep_fiji_image • visiumStitched
     

     
Create low-res images and scale factors from high-res Fiji output images

-    Source: R/prep_fiji_image.R
+    Source: R/prep_fiji_image.R
     
     

 
@@ -119,7 +119,8 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-26 18:56:54.068533 loading file /github/home/.cache/R/BiocFileCache/2ab3be94b44_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:08:50.448638 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d1b42d2d8_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -130,7 +131,8 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-26 18:56:56.879823 loading file /github/home/.cache/R/BiocFileCache/2ab78c3d33f_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:08:52.22303 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d4e4f1593_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
 sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
 sample_info$fiji_image_path <- temp[grep("png$", temp)]
 
@@ -157,6 +159,9 @@ 
Examples

 #> The following object is masked from ‘package:GenomicRanges’:
 #> 
 #>     subtract
+#> The following objects are masked from ‘package:testthat’:
+#> 
+#>     equals, is_less_than, not
 #> 
 #> Attaching package: ‘imager’
 #> The following object is masked from ‘package:magrittr’:
@@ -194,8 +199,8 @@ 
Examples

 
 #    In total, an image and scalefactors were written
 out_paths
-#> [1] "/tmp/RtmpZpoicf/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpZpoicf/Br2719/scalefactors_json.json" 
+#> [1] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//Rtmp355bXj/Br2719/tissue_lowres_image.png"
+#> [2] "/var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//Rtmp355bXj/Br2719/scalefactors_json.json"
@@ -210,7 +215,7 @@

Examples

-

Site built with pkgdown 2.1.0.9000.

+

Site built with pkgdown 2.1.0.

diff --git a/reference/rescale_fiji_inputs.html b/reference/rescale_fiji_inputs.html index a0dd603..d1faaa2 100644 --- a/reference/rescale_fiji_inputs.html +++ b/reference/rescale_fiji_inputs.html @@ -1,5 +1,5 @@ -Write same-scale hires images for input to Fiji — rescale_fiji_inputs • visiumStitchedWrite same-scale hires images for input to Fiji — rescale_fiji_inputs • visiumStitched

Write same-scale hires images for input to Fiji

- Source: R/rescale_fiji_inputs.R + Source: R/rescale_fiji_inputs.R
@@ -136,7 +136,8 @@

Examples

spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir ) -#> 2024-07-26 18:57:06.743077 loading file /github/home/.cache/R/BiocFileCache/2ab3be94b44_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1 +#> snapshotDate(): 2024-04-29 +#> 2024-07-26 17:08:59.47556 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d1b42d2d8_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1 sample_info$spaceranger_dir <- file.path( sr_dir, sample_info$capture_area, "outs", "spatial" ) @@ -147,7 +148,8 @@

Examples

spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"), exdir = fiji_dir ) -#> 2024-07-26 18:57:09.550149 loading file /github/home/.cache/R/BiocFileCache/2ab78c3d33f_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1 +#> snapshotDate(): 2024-04-29 +#> 2024-07-26 17:09:00.941612 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/1653d4e4f1593_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1 sample_info$fiji_xml_path <- temp[grep("xml$", temp)] sample_info$fiji_image_path <- temp[grep("png$", temp)] @@ -167,26 +169,28 @@

Examples

# Image are produced that are ready for alignment in Fiji list.files(out_dir) -#> [1] "Br2719" -#> [2] "Br2719.png" -#> [3] "Br2719.xml" -#> [4] "HDF5Array_dataset_creation_global_counter" -#> [5] "HDF5Array_dump" -#> [6] "HDF5Array_dump_log" -#> [7] "HDF5Array_dump_names_global_counter" -#> [8] "V13B23-283_A1" -#> [9] "V13B23-283_A1.png" -#> [10] "V13B23-283_C1" -#> [11] "V13B23-283_C1.png" -#> [12] "V13B23-283_D1" -#> [13] "V13B23-283_D1.png" -#> [14] "downlit" -#> [15] "file2fe529a4a29f" -#> [16] "file2fe53b60dfa6" -#> [17] "file2fe5671c217f" -#> [18] "file2fe5685d2769" -#> [19] "file2fe5731e1730" -#> [20] "file2fe58d498c1" +#> [1] "Br2719" +#> [2] "Br2719.png" +#> [3] "Br2719.xml" +#> [4] "HDF5Array_dataset_creation_global_counter" +#> [5] "HDF5Array_dump" +#> [6] "HDF5Array_dump_log" +#> [7] "HDF5Array_dump_names_global_counter" +#> [8] "V13B23-283_A1" +#> [9] "V13B23-283_A1.png" +#> [10] "V13B23-283_C1" +#> [11] "V13B23-283_C1.png" +#> [12] "V13B23-283_D1" +#> [13] "V13B23-283_D1.png" +#> [14] "downlit" +#> [15] "file13c41e43acfb" +#> [16] "file13c42f947a63" +#> [17] "file13c43a775d65" +#> [18] "file13c43cef11fc" +#> [19] "file13c46436efc2" +#> [20] "file13c474ab7f" +#> [21] "file13c47e1d4fe7" +#> [22] "rs-graphics-22aa88fb-9109-455f-a089-419e605f3ece" @@ -201,7 +205,7 @@

Examples

-

Site built with pkgdown 2.1.0.9000.

+

Site built with pkgdown 2.1.0.

diff --git a/reference/spe_to_seurat.html b/reference/spe_to_seurat.html index b114c0c..860ed46 100644 --- a/reference/spe_to_seurat.html +++ b/reference/spe_to_seurat.html @@ -1,5 +1,5 @@ -Convert a SpatialExperiment object to a Seurat object — spe_to_seurat • visiumStitchedConvert a SpatialExperiment object to a Seurat object — spe_to_seurat • visiumStitched

Convert a SpatialExperiment object to a Seurat object

- Source: R/spe_to_seurat.R + Source: R/spe_to_seurat.R
@@ -112,7 +112,8 @@

Author

Examples

## Download some example data
 spe <- spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
-#> 2024-07-26 18:57:16.840718 loading file /github/home/.cache/R/BiocFileCache/d7344586518_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:09:06.08056 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/15435f15b5f4_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
 
 ## Make the column names unique
 colnames(spe) <- spatialLIBD::add_key(spe)$key
@@ -143,7 +144,8 @@ 
Examples

 
 ## Example with an stitched SPE object
 spe_stitched <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 18:57:28.786952 loading file /github/home/.cache/R/BiocFileCache/2ab2fc23300_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> snapshotDate(): 2024-04-29
+#> 2024-07-26 17:09:12.688596 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/154352e7328f0_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
 seur_stitched <- spe_to_seurat(spe_stitched)
 #> Running 'as.Seurat(spe)'...
 #> Warning: Keys should be one or more alphanumeric characters followed by an underscore, setting key from PC to PC_
@@ -172,7 +174,7 @@ 
Examples
-

Site built with pkgdown 2.1.0.9000.

+

Site built with pkgdown 2.1.0.

diff --git a/reference/spot_plot-1.png b/reference/spot_plot-1.png deleted file mode 100644 index 719695e..0000000 Binary files a/reference/spot_plot-1.png and /dev/null differ diff --git a/reference/spot_plot-2.png b/reference/spot_plot-2.png deleted file mode 100644 index b272fd0..0000000 Binary files a/reference/spot_plot-2.png and /dev/null differ diff --git a/reference/spot_plot.html b/reference/spot_plot.html deleted file mode 100644 index ee3b814..0000000 --- a/reference/spot_plot.html +++ /dev/null @@ -1,232 +0,0 @@ - -Spatial plots of discrete or continuous features for stitched-together capture areas. — spot_plot • visiumStitched - - -
-
- - - -
-
-
-

Spatial plots of discrete or continuous features for stitched-together capture areas.

- Source: R/spot_plot.R - -
- -
-

This function is essentially a wrapper around spatialLIBD::vis_clus and -spatialLIBD::vis_gene, suitable for merged samples (each sample in the -SpatialExperiment 'spe' is a donor consisting of multiple capture areas, with -colData column 'exclude_overlapping' indicating overlapping spots to drop (to -prevent overplotting).

-
- -
- 
spot_plot(
-  spe,
-  sample_id,
-  image_id = "lowres",
-  title = sprintf("%s_%s", sample_id, var_name),
-  var_name,
-  multi_gene_method = c("z_score", "pca", "sparsity"),
-  include_legend = TRUE,
-  is_discrete,
-  colors = NULL,
-  assayname = "logcounts",
-  minCount = 0.5,
-  spatial = FALSE
-)
-
- -
-

Arguments

- - -
spe
-

A SpatialExperiment with colData column exclude_overlapping, -passed to spatialLIBD::vis_gene or spatialLIBD::vis_clus

- - -
sample_id
-

character(1) passed to sampleid in -spatialLIBD::vis_gene or spatialLIBD::vis_clus. Assumed to be a -donor, possibly consisting of several capture areas to plot at once

- - -
image_id
-

character(1) giving the name of the image (e.g. "lowres") to -plot, used both to determine an appropriate spot size and passed to -spatialLIBD::vis_gene or spatialLIBD::vis_clus

- - -
title
-

character(1) giving the title of the plot

- - -
var_name
-

character() passed to geneid for spatialLIBD::vis_gene -or character(1) passed to clustervar for spatialLIBD::vis_clus

- - -
multi_gene_method
-

A character(1): either "pca", "sparsity", or -"z_score". This parameter controls how multiple continuous variables are -combined for visualization, and only applies when var_name has length > 1 -and is_discrete is FALSE

- - -
include_legend
-

logical(1): if FALSE, remove the plot legend

- - -
is_discrete
-

logical(1): if TRUE, use spatialLIBD::vis_clus; -otherwise, use spatialLIBD::vis_gene

- - -
colors
-

character() of colors passed to colors for spatialLIBD::vis_clus -if is_discrete or otherwise to cont_colors for spatialLIBD::vis_gene

- - -
assayname
-

character(1) passed to spatialLIBD::vis_gene if -not is_discrete

- - -
minCount
-

numeric(1) passed to passed to spatialLIBD::vis_gene if -not is_discrete

- - -
spatial
-

logical(1) passed to sampleid in -spatialLIBD::vis_gene or spatialLIBD::vis_clus

- -
-
-

Value

-

A ggplot object containing a "spot plot" of the specified sample

-
-
-

Details

-

Spot sizes are almost consistent among donors, regardless of full- -resolution image dimensions, when title is NULL, include_legend is FALSE, -and the plot is saved to a square output (e.g. PDF with 7in width and -height). However, ggplot does not seem to scale plots of different aspect -ratios exactly consistently when writing to PDF (untested for other formats)

-
-
-

Author

-

Nicholas J. Eagles

-
- -
-

Examples

- 

-#   Grab an example SpatialExperiment and suppose all of its spots should be
-#   plotted (for spatialNAc, 'exclude_overlapping' will only have genuinely
-#   overlapping spots be TRUE)
-spe <- if (!exists("spe")) {
-    spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
-}
-#> 2024-07-26 14:35:15.038719 loading file /github/home/.cache/R/BiocFileCache/caf535d54f5_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
-spe$exclude_overlapping <- FALSE
-
-#   Plot age spatially for the first sample
-sample_id <- unique(spe$sample_id)[1]
-p <- spot_plot(
-    spe,
-    sample_id = sample_id,
-    title = sample_id, var_name = "age",
-    include_legend = TRUE, is_discrete = FALSE, minCount = 0,
-    assayname = "logcounts"
-)
-print(p)
-
-
-#    Define several markers for white matter
-white_matter_genes <- c(
-    "ENSG00000197971", "ENSG00000131095", "ENSG00000123560",
-    "ENSG00000171885"
-)
-
-#   Plot multiple white matter genes simultaneously for the first sample.
-#   Use the "pca" method for combining them
-p <- spot_plot(
-    spe,
-    sample_id = sample_id,
-    title = sample_id, var_name = white_matter_genes,
-    multi_gene_method = "pca", include_legend = TRUE, is_discrete = FALSE,
-    minCount = 0, assayname = "logcounts"
-)
-print(p)
-
-
-
-
- -
- - -
- - - - - - - -