diff --git a/articles/misc.html b/articles/misc.html index af45be1..72b55c9 100644 --- a/articles/misc.html +++ b/articles/misc.html @@ -103,7 +103,7 @@

Leonardo Health
lcolladotor@gmail.com -

30 July 2024

+

31 July 2024

Source: vignettes/misc.Rmd @@ -127,7 +127,7 @@

Load data
 ## Grab SpatialExperiment with normalized counts
 spe <- fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-30 14:29:12.692024 loading file /github/home/.cache/R/BiocFileCache/22015bb65a6_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-31 16:35:56.344088 loading file /github/home/.cache/R/BiocFileCache/3437663e19c_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
 
 ## Check that spe does contain the "logcounts" assay
 assayNames(spe)
diff --git a/articles/visiumStitched.html b/articles/visiumStitched.html
index 337c364..7bf8b2d 100644
--- a/articles/visiumStitched.html
+++ b/articles/visiumStitched.html
@@ -103,7 +103,7 @@ 
Leonardo
 Health

       
                   
-            
30 July 2024

+            
31 July 2024

       
       Source: vignettes/visiumStitched.Rmd
       
@@ -148,9 +148,10 @@ 
Citing visiumStitched#>   package version 0.99.0,
 #>   <http://www.bioconductor.org/packages/visiumStitched>.
 #> 
-#>   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>,
+#>   Eagles NJ, Bach S, Tippani M, Ravichandran P, 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>.
 #> 
 #> To see these entries in BibTeX format, use 'print(<citation>,
@@ -204,7 +205,7 @@ 
Preparing Experiment Informationtemp <- unzip(spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-30 14:29:41.753136 loading file /github/home/.cache/R/BiocFileCache/22077dbe5de_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-31 16:36:24.46471 loading file /github/home/.cache/R/BiocFileCache/3432f63584d_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -212,9 +213,9 @@ 
Preparing Experiment Information## Sample_info with paths to SpaceRanger output directories
 sample_info
 #>    group  capture_area                            spaceranger_dir
-#> 1 Br2719 V13B23-283_A1 /tmp/RtmpCw6poB/V13B23-283_A1/outs/spatial
-#> 2 Br2719 V13B23-283_C1 /tmp/RtmpCw6poB/V13B23-283_C1/outs/spatial
-#> 3 Br2719 V13B23-283_D1 /tmp/RtmpCw6poB/V13B23-283_D1/outs/spatial
+#> 1 Br2719 V13B23-283_A1 /tmp/Rtmp8Hmw1H/V13B23-283_A1/outs/spatial +#> 2 Br2719 V13B23-283_C1 /tmp/Rtmp8Hmw1H/V13B23-283_C1/outs/spatial +#> 3 Br2719 V13B23-283_D1 /tmp/Rtmp8Hmw1H/V13B23-283_D1/outs/spatial

Preparing Inputs to Fiji @@ -243,9 +244,9 @@

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/RtmpCw6poB/V1… 1.00 0.0825 -#> 2 Br2719 V13B23-283_C1 /tmp/RtmpCw6poB/V1… 1.00 0.0825 -#> 3 Br2719 V13B23-283_D1 /tmp/RtmpCw6poB/V1… 1 0.0825

+#> 1 Br2719 V13B23-283_A1 /tmp/Rtmp8Hmw1H/V1… 1.00 0.0825 +#> 2 Br2719 V13B23-283_C1 /tmp/Rtmp8Hmw1H/V1… 1.00 0.0825 +#> 3 Br2719 V13B23-283_D1 /tmp/Rtmp8Hmw1H/V1… 1 0.0825

Building a SpatialExperiment @@ -273,7 +274,7 @@

Creating Group-Level Samples
 fiji_dir <- tempdir()
 temp <- unzip(fetch_data("visiumStitched_brain_Fiji_out"), exdir = fiji_dir)
-#> 2024-07-30 14:29:56.171538 loading file /github/home/.cache/R/BiocFileCache/2207166af2d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-31 16:36:38.542475 loading file /github/home/.cache/R/BiocFileCache/34339e3b000_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 @@ -284,9 +285,9 @@

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/RtmpCw6poB/V1… 1.00 0.0825 -#> 2 Br2719 V13B23-283_C1 /tmp/RtmpCw6poB/V1… 1.00 0.0825 -#> 3 Br2719 V13B23-283_D1 /tmp/RtmpCw6poB/V1… 1 0.0825 +#> 1 Br2719 V13B23-283_A1 /tmp/Rtmp8Hmw1H/V1… 1.00 0.0825 +#> 2 Br2719 V13B23-283_C1 /tmp/Rtmp8Hmw1H/V1… 1.00 0.0825 +#> 3 Br2719 V13B23-283_D1 /tmp/Rtmp8Hmw1H/V1… 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 @@ -309,10 +310,10 @@

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/RtmpCw6poB/Br2719/tissue_positions.csv" +#> [1] "/tmp/Rtmp8Hmw1H/Br2719/tissue_positions.csv" prep_fiji_image(sample_info, out_dir = spe_input_dir) -#> [1] "/tmp/RtmpCw6poB/Br2719/tissue_lowres_image.png" -#> [2] "/tmp/RtmpCw6poB/Br2719/scalefactors_json.json" +#> [1] "/tmp/Rtmp8Hmw1H/Br2719/tissue_lowres_image.png" +#> [2] "/tmp/Rtmp8Hmw1H/Br2719/scalefactors_json.json"

Constructing the Object @@ -353,11 +354,11 @@

Constructing the Object coords_dir = spe_input_dir, reference_gtf = gtf_cache ) #> Building SpatialExperiment using capture area as sample ID -#> 2024-07-30 14:29:59.440808 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-07-30 14:30:06.58617 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-07-30 14:30:07.017973 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-07-30 14:30:07.4117 rtracklayer::import: reading the reference GTF file -#> 2024-07-30 14:30:39.178627 adding gene information to the SPE object +#> 2024-07-31 16:36:41.777273 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-07-31 16:36:48.727558 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-07-31 16:36:49.132517 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-07-31 16:36:49.487245 rtracklayer::import: reading the reference GTF file +#> 2024-07-31 16:37:20.783861 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() @@ -365,7 +366,7 @@

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. -#> 2024-07-30 14:30:39.410285 adding information used by spatialLIBD +#> 2024-07-31 16:37:21.018672 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. @@ -529,7 +530,7 @@

Downstream applications
 ## Grab SpatialExperiment with normalized counts
 spe_norm <- fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-30 14:30:45.495779 loading file /github/home/.cache/R/BiocFileCache/22015bb65a6_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-31 16:37:27.865576 loading file /github/home/.cache/R/BiocFileCache/3437663e19c_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
 assayNames(spe_norm)
 #> [1] "counts"    "logcounts"
 
@@ -674,9 +675,9 @@ 
Reproducibilitylibrary("knitr")
 knit("visiumStitched.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-07-30 14:30:49 UTC"
+
#> [1] "2024-07-31 16:37:32 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.399 mins
+
#> Time difference of 1.384 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -688,7 +689,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-07-30
+#>  date     2024-07-31
 #>  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -798,7 +799,7 @@ 
Reproducibility#>  lazyeval               0.2.2      2019-03-15 [1] RSPM (R 4.4.0)
 #>  leiden                 0.4.3.1    2023-11-17 [1] RSPM (R 4.4.0)
 #>  lifecycle              1.0.4      2023-11-07 [2] RSPM (R 4.4.0)
-#>  limma                  3.61.5     2024-07-22 [1] Bioconductor 3.20 (R 4.4.1)
+#>  limma                  3.61.6     2024-07-29 [1] Bioconductor 3.20 (R 4.4.1)
 #>  listenv                0.9.1      2024-01-29 [1] RSPM (R 4.4.0)
 #>  lmtest                 0.9-40     2022-03-21 [1] RSPM (R 4.4.0)
 #>  locfit                 1.5-9.10   2024-06-24 [1] RSPM (R 4.4.0)
@@ -879,7 +880,7 @@ 
Reproducibility#>  SingleCellExperiment * 1.27.2     2024-05-24 [1] Bioconductor 3.20 (R 4.4.0)
 #>  sp                     2.1-4      2024-04-30 [1] RSPM (R 4.4.0)
 #>  spam                   2.10-0     2023-10-23 [1] RSPM (R 4.4.0)
-#>  SparseArray            1.5.26     2024-07-25 [1] Bioconductor 3.20 (R 4.4.1)
+#>  SparseArray            1.5.27     2024-07-29 [1] Bioconductor 3.20 (R 4.4.1)
 #>  sparseMatrixStats      1.17.2     2024-06-12 [1] Bioconductor 3.20 (R 4.4.0)
 #>  SpatialExperiment    * 1.15.1     2024-06-20 [1] Bioconductor 3.20 (R 4.4.0)
 #>  spatialLIBD          * 1.17.8     2024-07-30 [1] Github (LieberInstitute/spatialLIBD@c82c789)
@@ -911,7 +912,7 @@ 
Reproducibility#>  vipor                  0.4.7      2023-12-18 [1] RSPM (R 4.4.0)
 #>  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)
-#>  visiumStitched       * 0.99.0     2024-07-30 [1] Bioconductor
+#>  visiumStitched       * 0.99.0     2024-07-31 [1] Bioconductor
 #>  vroom                  1.6.5      2023-12-05 [1] RSPM (R 4.4.0)
 #>  withr                  3.0.0      2024-01-16 [2] RSPM (R 4.4.0)
 #>  xfun                   0.46       2024-07-18 [2] RSPM (R 4.4.0)
diff --git a/authors.html b/authors.html
index d969f35..6e083ec 100644
--- a/authors.html
+++ b/authors.html
@@ -90,14 +90,14 @@ 
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, Miller RA, Hyde TM, Page SC, Martinowich K, Collado-Torres L (2024). +

Eagles NJ, Bach S, Tippani M, Ravichandran P, 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 Ryan A. Miller 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 Prashanthi Ravichandran 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},
diff --git a/index.html b/index.html
index cf7783a..e5c7999 100644
--- a/index.html
+++ b/index.html
@@ -105,7 +105,7 @@ 
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 18:36:29.721855 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/154352e7328f0_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-31 12:06:58.719486 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
@@ -168,16 +168,17 @@ 
Citation#>     doi = {10.18129/B9.bioc.visiumStitched},
 #>   }
 #> 
-#>   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>,
+#>   Eagles NJ, Bach S, Tippani M, Ravichandran P, 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>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Article{,
 #>     title = {visiumStitched},
-#>     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},
+#>     author = {Nicholas J. Eagles and Svitlana Bach and Madhavi Tippani and Prashanthi Ravichandran 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},
diff --git a/pkgdown.yml b/pkgdown.yml
index a264979..4745bbb 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,4 +4,4 @@ pkgdown_sha: 6f01c9267a1cee263216cec38eea10017d751dd8
 articles:
   misc: misc.html
   visiumStitched: visiumStitched.html
-last_built: 2024-07-30T14:26Z
+last_built: 2024-07-31T16:33Z
diff --git a/reference/add_array_coords.html b/reference/add_array_coords.html
index af18b18..15b4581 100644
--- a/reference/add_array_coords.html
+++ b/reference/add_array_coords.html
@@ -135,7 +135,7 @@ 
Author

     

     
Examples

     
spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-30 14:26:55.737017 loading file /github/home/.cache/R/BiocFileCache/22015bb65a6_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-31 16:33:39.776738 loading file /github/home/.cache/R/BiocFileCache/3437663e19c_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
 
 ########################################################################
 #   Prepare sample_info
@@ -151,7 +151,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-30 14:27:00.04017 loading file /github/home/.cache/R/BiocFileCache/22077dbe5de_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-31 16:33:43.916949 loading file /github/home/.cache/R/BiocFileCache/3432f63584d_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -162,7 +162,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-30 14:27:02.525698 loading file /github/home/.cache/R/BiocFileCache/2207166af2d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-31 16:33:46.225532 loading file /github/home/.cache/R/BiocFileCache/34339e3b000_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)]
 
@@ -172,10 +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/Rtmp1TnElt/Br2719/tissue_positions.csv"
+#> [1] "/tmp/RtmpqzYIEL/Br2719/tissue_positions.csv"
 prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/Rtmp1TnElt/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/Rtmp1TnElt/Br2719/scalefactors_json.json" 
+#> [1] "/tmp/RtmpqzYIEL/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/RtmpqzYIEL/Br2719/scalefactors_json.json" 
 
 ########################################################################
 #   Add array coordinates
diff --git a/reference/add_overlap_info.html b/reference/add_overlap_info.html
index 4d49b21..bb71780 100644
--- a/reference/add_overlap_info.html
+++ b/reference/add_overlap_info.html
@@ -115,7 +115,7 @@ 
Author

     

     
Examples

     
spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-30 14:27:16.425884 loading file /github/home/.cache/R/BiocFileCache/22015bb65a6_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-31 16:33:59.76725 loading file /github/home/.cache/R/BiocFileCache/3437663e19c_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
 
 #    Find the mean of the 'sum_umi' metric by capture area to understand
 #    which capture areas will be excluded in regions of overlap
diff --git a/reference/build_spe.html b/reference/build_spe.html
index a1a2c82..e76fccd 100644
--- a/reference/build_spe.html
+++ b/reference/build_spe.html
@@ -159,7 +159,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-30 14:27:21.063389 loading file /github/home/.cache/R/BiocFileCache/22077dbe5de_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-31 16:34:04.276682 loading file /github/home/.cache/R/BiocFileCache/3432f63584d_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -170,7 +170,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-30 14:27:23.635112 loading file /github/home/.cache/R/BiocFileCache/2207166af2d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-31 16:34:06.842666 loading file /github/home/.cache/R/BiocFileCache/34339e3b000_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)]
 
@@ -180,10 +180,10 @@ 
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/Rtmp1TnElt/Br2719/tissue_positions.csv"
+#> [1] "/tmp/RtmpqzYIEL/Br2719/tissue_positions.csv"
 prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/Rtmp1TnElt/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/Rtmp1TnElt/Br2719/scalefactors_json.json" 
+#> [1] "/tmp/RtmpqzYIEL/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/RtmpqzYIEL/Br2719/scalefactors_json.json" 
 
 ########################################################################
 #   Build the SpatialExperiment
@@ -209,14 +209,14 @@ 
Examples

     coords_dir = spe_input_dir, reference_gtf = gtf_cache
 )
 #> Building SpatialExperiment using capture area as sample ID
-#> 2024-07-30 14:27:29.766322 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
-#> 2024-07-30 14:27:35.874853 read10xVisiumAnalysis: reading analysis output from SpaceRanger
-#> 2024-07-30 14:27:36.325266 add10xVisiumAnalysis: adding analysis output from SpaceRanger
-#> 2024-07-30 14:27:36.668733 rtracklayer::import: reading the reference GTF file
-#> 2024-07-30 14:28:06.209781 adding gene information to the SPE object
+#> 2024-07-31 16:34:12.895255 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
+#> 2024-07-31 16:34:19.813821 read10xVisiumAnalysis: reading analysis output from SpaceRanger
+#> 2024-07-31 16:34:20.128523 add10xVisiumAnalysis: adding analysis output from SpaceRanger
+#> 2024-07-31 16:34:20.441931 rtracklayer::import: reading the reference GTF file
+#> 2024-07-31 16:34:49.53816 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.
-#> 2024-07-30 14:28:06.450191 adding information used by spatialLIBD
+#> 2024-07-31 16:34:49.765046 adding information used by spatialLIBD
 #> Overwriting imgData(spe) with merged images (one per group)
 
 ## Let's explore the stitched SpatialExperiment object
diff --git a/reference/prep_fiji_coords.html b/reference/prep_fiji_coords.html
index c0c411f..99db503 100644
--- a/reference/prep_fiji_coords.html
+++ b/reference/prep_fiji_coords.html
@@ -121,7 +121,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-30 14:28:10.163207 loading file /github/home/.cache/R/BiocFileCache/22077dbe5de_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-31 16:34:53.4914 loading file /github/home/.cache/R/BiocFileCache/3432f63584d_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -132,7 +132,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-30 14:28:12.804425 loading file /github/home/.cache/R/BiocFileCache/2207166af2d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-31 16:34:55.984684 loading file /github/home/.cache/R/BiocFileCache/34339e3b000_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)]
 
@@ -142,7 +142,7 @@ 
Examples

 spe_input_dir <- tempdir()
 out_file <- prep_fiji_coords(sample_info, out_dir = spe_input_dir)
 out_file
-#> [1] "/tmp/Rtmp1TnElt/Br2719/tissue_positions.csv"
+#> [1] "/tmp/RtmpqzYIEL/Br2719/tissue_positions.csv"
 
 #    A file of spatial coordinates for the stitched Br2719 was produced
 readr::read_csv(out_file)
diff --git a/reference/prep_fiji_image.html b/reference/prep_fiji_image.html
index 7295195..0df1b0f 100644
--- a/reference/prep_fiji_image.html
+++ b/reference/prep_fiji_image.html
@@ -129,7 +129,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-30 14:28:21.316194 loading file /github/home/.cache/R/BiocFileCache/22077dbe5de_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-31 16:35:04.62327 loading file /github/home/.cache/R/BiocFileCache/3432f63584d_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -140,7 +140,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-30 14:28:23.795841 loading file /github/home/.cache/R/BiocFileCache/2207166af2d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-31 16:35:07.141318 loading file /github/home/.cache/R/BiocFileCache/34339e3b000_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)]
 
@@ -204,8 +204,8 @@ 
Examples

 
 #    In total, an image and scalefactors were written
 out_paths
-#> [1] "/tmp/Rtmp1TnElt/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/Rtmp1TnElt/Br2719/scalefactors_json.json" 
+#> [1] "/tmp/RtmpqzYIEL/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/RtmpqzYIEL/Br2719/scalefactors_json.json" 
 

     

   

diff --git a/reference/rescale_fiji_inputs.html b/reference/rescale_fiji_inputs.html
index 8a65b55..12f29fc 100644
--- a/reference/rescale_fiji_inputs.html
+++ b/reference/rescale_fiji_inputs.html
@@ -146,7 +146,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-30 14:28:32.641985 loading file /github/home/.cache/R/BiocFileCache/22077dbe5de_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-31 16:35:17.374339 loading file /github/home/.cache/R/BiocFileCache/3432f63584d_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -157,7 +157,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-30 14:28:35.127847 loading file /github/home/.cache/R/BiocFileCache/2207166af2d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-31 16:35:20.106255 loading file /github/home/.cache/R/BiocFileCache/34339e3b000_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)]
 
@@ -191,12 +191,12 @@ 
Examples

 #> [12] "V13B23-283_D1"                            
 #> [13] "V13B23-283_D1.png"                        
 #> [14] "downlit"                                  
-#> [15] "file303c1508f472"                         
-#> [16] "file303c160928a9"                         
-#> [17] "file303c29f27fbf"                         
-#> [18] "file303c56d4ef75"                         
-#> [19] "file303c58484fb5"                         
-#> [20] "file303cbacb4d3"                          
+#> [15] "file315f108b0265"                         
+#> [16] "file315f123493d9"                         
+#> [17] "file315f3ce1338c"                         
+#> [18] "file315f4604ec8"                          
+#> [19] "file315f66127af2"                         
+#> [20] "file315fb5b2d96"
diff --git a/reference/spe_to_seurat.html b/reference/spe_to_seurat.html index 1b215c6..c022175 100644 --- a/reference/spe_to_seurat.html +++ b/reference/spe_to_seurat.html @@ -122,7 +122,7 @@

Author

Examples

## Download some example data
 spe <- spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
-#> 2024-07-30 14:28:43.619292 loading file /github/home/.cache/R/BiocFileCache/d267b63822f_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-07-31 16:35:26.924466 loading file /github/home/.cache/R/BiocFileCache/e48a7e5874_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
 
 ## Make the column names unique
 colnames(spe) <- spatialLIBD::add_key(spe)$key
@@ -153,7 +153,7 @@ 
Examples

 
 ## Example with an stitched SPE object
 spe_stitched <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-30 14:28:54.131247 loading file /github/home/.cache/R/BiocFileCache/22015bb65a6_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-31 16:35:39.167713 loading file /github/home/.cache/R/BiocFileCache/3437663e19c_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_