diff --git a/articles/visiumStitched.html b/articles/visiumStitched.html index 8a2c105..af42de3 100644 --- a/articles/visiumStitched.html +++ b/articles/visiumStitched.html @@ -187,7 +187,7 @@

Preparing Experiment Informationsr_dir <- tempdir() temp <- unzip(spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir) -#> 2024-07-26 18:35:25.661588 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1 +#> 2024-07-26 18:51:32.383722 loading file /github/home/.cache/R/BiocFileCache/2aa55fbec4f_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1 sample_info$spaceranger_dir <- file.path( sr_dir, sample_info$capture_area, "outs", "spatial" ) @@ -197,9 +197,9 @@

Preparing Experiment Information#> # A tibble: 3 × 3 #> group capture_area spaceranger_dir #> <chr> <chr> <chr> -#> 1 Br2719 V13B23-283_A1 /tmp/RtmpzaGKBG/V13B23-283_A1/outs/spatial -#> 2 Br2719 V13B23-283_C1 /tmp/RtmpzaGKBG/V13B23-283_C1/outs/spatial -#> 3 Br2719 V13B23-283_D1 /tmp/RtmpzaGKBG/V13B23-283_D1/outs/spatial +#> 1 Br2719 V13B23-283_A1 /tmp/RtmplXA9Gr/V13B23-283_A1/outs/spatial +#> 2 Br2719 V13B23-283_C1 /tmp/RtmplXA9Gr/V13B23-283_C1/outs/spatial +#> 3 Br2719 V13B23-283_D1 /tmp/RtmplXA9Gr/V13B23-283_D1/outs/spatial

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

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

+#> 1 Br2719 V13B23-283_A1 /tmp/RtmplXA9Gr/V1… 1.00 0.0825 +#> 2 Br2719 V13B23-283_C1 /tmp/RtmplXA9Gr/V1… 1.00 0.0825 +#> 3 Br2719 V13B23-283_D1 /tmp/RtmplXA9Gr/V1… 1 0.0825

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

Creating Group-Level Samples
 fiji_dir <- tempdir()
 temp <- unzip(fetch_data("visiumStitched_brain_Fiji_out"), exdir = fiji_dir)
-#> 2024-07-26 18:35:40.787131 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:51:47.466255 loading file /github/home/.cache/R/BiocFileCache/2aa6ee73ff2_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 +269,9 @@

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/RtmpzaGKBG/V1… 1.00 0.0825 -#> 2 Br2719 V13B23-283_C1 /tmp/RtmpzaGKBG/V1… 1.00 0.0825 -#> 3 Br2719 V13B23-283_D1 /tmp/RtmpzaGKBG/V1… 1 0.0825 +#> 1 Br2719 V13B23-283_A1 /tmp/RtmplXA9Gr/V1… 1.00 0.0825 +#> 2 Br2719 V13B23-283_C1 /tmp/RtmplXA9Gr/V1… 1.00 0.0825 +#> 3 Br2719 V13B23-283_D1 /tmp/RtmplXA9Gr/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 @@ -294,10 +294,10 @@

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/RtmpzaGKBG/Br2719/tissue_positions.csv" +#> [1] "/tmp/RtmplXA9Gr/Br2719/tissue_positions.csv" prep_fiji_image(sample_info, out_dir = spe_input_dir) -#> [1] "/tmp/RtmpzaGKBG/Br2719/tissue_lowres_image.png" -#> [2] "/tmp/RtmpzaGKBG/Br2719/scalefactors_json.json" +#> [1] "/tmp/RtmplXA9Gr/Br2719/tissue_lowres_image.png" +#> [2] "/tmp/RtmplXA9Gr/Br2719/scalefactors_json.json"

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

Constructing the Object coords_dir = spe_input_dir, reference_gtf = gtf_cache ) #> Building SpatialExperiment using capture area as sample ID -#> 2024-07-26 18:35:44.035847 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-07-26 18:35:50.972202 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-07-26 18:35:51.371096 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-07-26 18:35:51.720437 rtracklayer::import: reading the reference GTF file -#> 2024-07-26 18:36:22.768934 adding gene information to the SPE object +#> 2024-07-26 18:51:50.597136 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-07-26 18:51:57.491656 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-07-26 18:51:57.884006 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-07-26 18:51:58.228596 rtracklayer::import: reading the reference GTF file +#> 2024-07-26 18:52:29.933243 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 +350,7 @@

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 18:36:22.997012 adding information used by spatialLIBD +#> 2024-07-26 18:52:30.162581 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 +512,7 @@

A note on normalization
 ## Grab SpatialExperiment with normalized counts
 spe_norm <- fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 18:36:31.772382 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:52:38.952264 loading file /github/home/.cache/R/BiocFileCache/2aa28e6ad0c_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)
@@ -689,9 +689,9 @@ 
Reproducibilitylibrary("knitr")
 knit("visiumStitched.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-07-26 18:36:39 UTC"
+
#> [1] "2024-07-26 18:52:46 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.458 mins
+
#> Time difference of 1.468 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/pkgdown.yml b/pkgdown.yml
index 2f47c31..f90e1dd 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,4 +3,4 @@ pkgdown: 2.1.0.9000
 pkgdown_sha: 6f01c9267a1cee263216cec38eea10017d751dd8
 articles:
   visiumStitched: visiumStitched.html
-last_built: 2024-07-26T18:32Z
+last_built: 2024-07-26T18:49Z
diff --git a/reference/add_array_coords.html b/reference/add_array_coords.html
index 18bd0a1..52e7844 100644
--- a/reference/add_array_coords.html
+++ b/reference/add_array_coords.html
@@ -125,7 +125,7 @@ 
Author

     

     
Examples

     
spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 18:33:11.689703 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:49:17.838443 loading file /github/home/.cache/R/BiocFileCache/2aa28e6ad0c_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
 
 ########################################################################
 #   Prepare sample_info
@@ -141,7 +141,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-26 18:33:15.777896 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:49:21.94464 loading file /github/home/.cache/R/BiocFileCache/2aa55fbec4f_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -152,7 +152,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-26 18:33:18.010393 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:49:24.292386 loading file /github/home/.cache/R/BiocFileCache/2aa6ee73ff2_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 +162,10 @@ 
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/Rtmp4mylSN/Br2719/tissue_positions.csv"
+#> [1] "/tmp/Rtmpzr5hP7/Br2719/tissue_positions.csv"
 prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/Rtmp4mylSN/Br2719/scalefactors_json.json" 
+#> [1] "/tmp/Rtmpzr5hP7/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/Rtmpzr5hP7/Br2719/scalefactors_json.json" 
 
 ########################################################################
 #   Add array coordinates
diff --git a/reference/add_overlap_info.html b/reference/add_overlap_info.html
index 301a874..11f5382 100644
--- a/reference/add_overlap_info.html
+++ b/reference/add_overlap_info.html
@@ -105,7 +105,7 @@ 
Author

     

     
Examples

     
spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 18:33:31.371027 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:49:38.107696 loading file /github/home/.cache/R/BiocFileCache/2aa28e6ad0c_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 536097a..b70635c 100644
--- a/reference/build_spe.html
+++ b/reference/build_spe.html
@@ -149,7 +149,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-26 18:33:35.64846 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:49:42.556157 loading file /github/home/.cache/R/BiocFileCache/2aa55fbec4f_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -160,7 +160,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-26 18:33:38.17873 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:49:44.972171 loading file /github/home/.cache/R/BiocFileCache/2aa6ee73ff2_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 +170,10 @@ 
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/Rtmp4mylSN/Br2719/tissue_positions.csv"
+#> [1] "/tmp/Rtmpzr5hP7/Br2719/tissue_positions.csv"
 prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/Rtmp4mylSN/Br2719/scalefactors_json.json" 
+#> [1] "/tmp/Rtmpzr5hP7/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/Rtmpzr5hP7/Br2719/scalefactors_json.json" 
 
 ########################################################################
 #   Build the SpatialExperiment
@@ -199,14 +199,14 @@ 
Examples

     coords_dir = spe_input_dir, reference_gtf = gtf_cache
 )
 #> Building SpatialExperiment using capture area as sample ID
-#> 2024-07-26 18:33:44.254454 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
-#> 2024-07-26 18:33:50.227049 read10xVisiumAnalysis: reading analysis output from SpaceRanger
-#> 2024-07-26 18:33:50.628412 add10xVisiumAnalysis: adding analysis output from SpaceRanger
-#> 2024-07-26 18:33:50.944881 rtracklayer::import: reading the reference GTF file
-#> 2024-07-26 18:34:19.387128 adding gene information to the SPE object
+#> 2024-07-26 18:49:51.109622 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
+#> 2024-07-26 18:49:57.268413 read10xVisiumAnalysis: reading analysis output from SpaceRanger
+#> 2024-07-26 18:49:57.670396 add10xVisiumAnalysis: adding analysis output from SpaceRanger
+#> 2024-07-26 18:49:57.989657 rtracklayer::import: reading the reference GTF file
+#> 2024-07-26 18:50:26.534192 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 18:34:19.614623 adding information used by spatialLIBD
+#> 2024-07-26 18:50:26.768991 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/dot-fit_to_array.html b/reference/dot-fit_to_array.html
index 4d47a2f..a636d29 100644
--- a/reference/dot-fit_to_array.html
+++ b/reference/dot-fit_to_array.html
@@ -84,7 +84,7 @@ 
Arguments

 

     

     
Value

-    
A tibble with modified array_row + array_col
+    
A tibble with modified array_row + array_col
 columns, as well as new pxl_row_in_fullres_rounded and
 pxl_col_in_fullres_rounded columns representing the pixel coordinates
 rounded to the nearest exact array coordinates.

diff --git a/reference/prep_fiji_coords.html b/reference/prep_fiji_coords.html
index 174c5c6..e8d3bc3 100644
--- a/reference/prep_fiji_coords.html
+++ b/reference/prep_fiji_coords.html
@@ -111,7 +111,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-26 18:34:23.176996 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:50:30.321649 loading file /github/home/.cache/R/BiocFileCache/2aa55fbec4f_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -122,7 +122,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-26 18:34:25.562983 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:50:32.594832 loading file /github/home/.cache/R/BiocFileCache/2aa6ee73ff2_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 +132,7 @@ 
Examples

 spe_input_dir <- tempdir()
 out_file <- prep_fiji_coords(sample_info, out_dir = spe_input_dir)
 out_file
-#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_positions.csv"
+#> [1] "/tmp/Rtmpzr5hP7/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 03c135c..a01e0c0 100644
--- a/reference/prep_fiji_image.html
+++ b/reference/prep_fiji_image.html
@@ -119,7 +119,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-26 18:34:34.360621 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:50:41.352124 loading file /github/home/.cache/R/BiocFileCache/2aa55fbec4f_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -130,7 +130,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-26 18:34:36.775245 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:50:43.773302 loading file /github/home/.cache/R/BiocFileCache/2aa6ee73ff2_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)]
 
@@ -194,8 +194,8 @@ 
Examples

 
 #    In total, an image and scalefactors were written
 out_paths
-#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/Rtmp4mylSN/Br2719/scalefactors_json.json" 
+#> [1] "/tmp/Rtmpzr5hP7/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/Rtmpzr5hP7/Br2719/scalefactors_json.json" 
 

     

   
diff --git a/reference/rescale_fiji_inputs.html b/reference/rescale_fiji_inputs.html
index a1e88b2..6ec56de 100644
--- a/reference/rescale_fiji_inputs.html
+++ b/reference/rescale_fiji_inputs.html
@@ -114,7 +114,7 @@ 
Arguments

 
     

     
Value

-    
A tibble: a copy of sample_info with
+    
A tibble: a copy of sample_info with
 additional columns
 intra_group_scalar and group_hires_scalef.

     

@@ -136,7 +136,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-26 18:34:45.683137 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:50:52.406342 loading file /github/home/.cache/R/BiocFileCache/2aa55fbec4f_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
 sample_info$spaceranger_dir <- file.path(
     sr_dir, sample_info$capture_area, "outs", "spatial"
 )
@@ -147,7 +147,7 @@ 
Examples

     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
     exdir = fiji_dir
 )
-#> 2024-07-26 18:34:48.090167 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:50:54.830088 loading file /github/home/.cache/R/BiocFileCache/2aa6ee73ff2_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)]
 
@@ -181,12 +181,12 @@ 
Examples

 #> [12] "V13B23-283_D1"                            
 #> [13] "V13B23-283_D1.png"                        
 #> [14] "downlit"                                  
-#> [15] "file2fe526234c6c"                         
-#> [16] "file2fe537e3e75"                          
-#> [17] "file2fe5486b0347"                         
-#> [18] "file2fe54de20e80"                         
-#> [19] "file2fe57fc3ec5"                          
-#> [20] "file2fe5b855f"                            
+#> [15] "file2fe23e6ca58c"                         
+#> [16] "file2fe24dac9670"                         
+#> [17] "file2fe250c4fb13"                         
+#> [18] "file2fe25edf013a"                         
+#> [19] "file2fe2670898a4"                         
+#> [20] "file2fe2799b01c7"
diff --git a/reference/spe_to_seurat.html b/reference/spe_to_seurat.html index 721c970..8f0ced8 100644 --- a/reference/spe_to_seurat.html +++ b/reference/spe_to_seurat.html @@ -112,7 +112,7 @@

Author

Examples

## Download some example data
 spe <- spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
-#> 2024-07-26 18:34:54.769072 loading file /github/home/.cache/R/BiocFileCache/d74272cc73b_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-07-26 18:51:01.266356 loading file /github/home/.cache/R/BiocFileCache/d72fb1846a_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
 
 ## Make the column names unique
 colnames(spe) <- spatialLIBD::add_key(spe)$key
@@ -143,7 +143,7 @@ 
Examples

 
 ## Example with an stitched SPE object
 spe_stitched <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 18:35:05.705695 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:51:12.427213 loading file /github/home/.cache/R/BiocFileCache/2aa28e6ad0c_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_