From 93b10d21bc901da373004185f7844130ea8b00cd Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Fri, 26 Jul 2024 23:04:30 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/visiumStitched@8a38c09a01d411bc8759f99e6f3a12da1099fdc8?= =?UTF-8?q?=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/visiumStitched.html | 46 +++++++++++++++--------------- index.html | 3 +- pkgdown.yml | 2 +- reference/add_array_coords.html | 12 ++++---- reference/add_overlap_info.html | 2 +- reference/build_spe.html | 22 +++++++------- reference/prep_fiji_coords.html | 6 ++-- reference/prep_fiji_image.html | 8 +++--- reference/rescale_fiji_inputs.html | 16 +++++------ reference/spe_to_seurat.html | 4 +-- 10 files changed, 61 insertions(+), 60 deletions(-) diff --git a/articles/visiumStitched.html b/articles/visiumStitched.html index 602f2ff..bd0d660 100644 --- a/articles/visiumStitched.html +++ b/articles/visiumStitched.html @@ -193,7 +193,7 @@

Preparing Experiment Informationsr_dir <- tempdir() temp <- unzip(spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"), exdir = sr_dir) -#> 2024-07-26 22:21:36.106136 loading file /github/home/.cache/R/BiocFileCache/29538a254d3_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1 +#> 2024-07-26 23:03:09.504999 loading file /github/home/.cache/R/BiocFileCache/2969246b12_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1 sample_info$spaceranger_dir <- file.path( sr_dir, sample_info$capture_area, "outs", "spatial" ) @@ -203,9 +203,9 @@

Preparing Experiment Information#> # A tibble: 3 × 3 #> group capture_area spaceranger_dir #> <chr> <chr> <chr> -#> 1 Br2719 V13B23-283_A1 /tmp/Rtmp0RpjQW/V13B23-283_A1/outs/spatial -#> 2 Br2719 V13B23-283_C1 /tmp/Rtmp0RpjQW/V13B23-283_C1/outs/spatial -#> 3 Br2719 V13B23-283_D1 /tmp/Rtmp0RpjQW/V13B23-283_D1/outs/spatial +#> 1 Br2719 V13B23-283_A1 /tmp/RtmpvPLbny/V13B23-283_A1/outs/spatial +#> 2 Br2719 V13B23-283_C1 /tmp/RtmpvPLbny/V13B23-283_C1/outs/spatial +#> 3 Br2719 V13B23-283_D1 /tmp/RtmpvPLbny/V13B23-283_D1/outs/spatial

Preparing Inputs to Fiji @@ -234,9 +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/Rtmp0RpjQW/V1… 1.00 0.0825 -#> 2 Br2719 V13B23-283_C1 /tmp/Rtmp0RpjQW/V1… 1.00 0.0825 -#> 3 Br2719 V13B23-283_D1 /tmp/Rtmp0RpjQW/V1… 1 0.0825

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

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

Creating Group-Level Samples
 fiji_dir <- tempdir()
 temp <- unzip(fetch_data("visiumStitched_brain_Fiji_out"), exdir = fiji_dir)
-#> 2024-07-26 22:21:50.047297 loading file /github/home/.cache/R/BiocFileCache/295ea19ac5_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 23:03:23.45545 loading file /github/home/.cache/R/BiocFileCache/2966a8bc07_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 @@ -275,9 +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/Rtmp0RpjQW/V1… 1.00 0.0825 -#> 2 Br2719 V13B23-283_C1 /tmp/Rtmp0RpjQW/V1… 1.00 0.0825 -#> 3 Br2719 V13B23-283_D1 /tmp/Rtmp0RpjQW/V1… 1 0.0825 +#> 1 Br2719 V13B23-283_A1 /tmp/RtmpvPLbny/V1… 1.00 0.0825 +#> 2 Br2719 V13B23-283_C1 /tmp/RtmpvPLbny/V1… 1.00 0.0825 +#> 3 Br2719 V13B23-283_D1 /tmp/RtmpvPLbny/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 @@ -300,10 +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/Rtmp0RpjQW/Br2719/tissue_positions.csv" +#> [1] "/tmp/RtmpvPLbny/Br2719/tissue_positions.csv" prep_fiji_image(sample_info, out_dir = spe_input_dir) -#> [1] "/tmp/Rtmp0RpjQW/Br2719/tissue_lowres_image.png" -#> [2] "/tmp/Rtmp0RpjQW/Br2719/scalefactors_json.json" +#> [1] "/tmp/RtmpvPLbny/Br2719/tissue_lowres_image.png" +#> [2] "/tmp/RtmpvPLbny/Br2719/scalefactors_json.json"

Constructing the Object @@ -344,11 +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 22:21:53.203693 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-07-26 22:22:00.15327 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-07-26 22:22:00.564512 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-07-26 22:22:00.917032 rtracklayer::import: reading the reference GTF file -#> 2024-07-26 22:22:31.910214 adding gene information to the SPE object +#> 2024-07-26 23:03:26.734109 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-07-26 23:03:33.676753 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-07-26 23:03:34.075078 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-07-26 23:03:34.433758 rtracklayer::import: reading the reference GTF file +#> 2024-07-26 23:04:05.255478 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() @@ -356,7 +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 22:22:32.139463 adding information used by spatialLIBD +#> 2024-07-26 23:04:05.482682 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. @@ -518,7 +518,7 @@

A note on normalization
 ## Grab SpatialExperiment with normalized counts
 spe_norm <- fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 22:22:40.364662 loading file /github/home/.cache/R/BiocFileCache/29568707510_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 23:04:13.677124 loading file /github/home/.cache/R/BiocFileCache/29632475d0e_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)
@@ -707,9 +707,9 @@ 
Reproducibilitylibrary("knitr")
 knit("visiumStitched.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-07-26 22:22:46 UTC"
+
#> [1] "2024-07-26 23:04:19 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.412 mins
+
#> Time difference of 1.406 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/index.html b/index.html
index 15d5dce..4c9fc66 100644
--- a/index.html
+++ b/index.html
@@ -93,7 +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 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
+#> 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
 
 ## Explore the stitched data
 spe
@@ -237,6 +237,7 @@ 
Developers

 

 
Dev status

 
    
+
  • DOI
    • 
 
  • GitHub issues
    • 
 
  • GitHub pulls
    • 
 
  • Lifecycle: stable
    • 
diff --git a/pkgdown.yml b/pkgdown.yml
index 08d11d4..027f54d 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: 2024-07-26T22:18Z
+last_built: 2024-07-26T23:00Z
diff --git a/reference/add_array_coords.html b/reference/add_array_coords.html
index cf03271..06d1e8c 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 22:19:17.901341 loading file /github/home/.cache/R/BiocFileCache/29568707510_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 23:00:53.414296 loading file /github/home/.cache/R/BiocFileCache/29632475d0e_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 22:19:22.117464 loading file /github/home/.cache/R/BiocFileCache/29538a254d3_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 23:00:57.438135 loading file /github/home/.cache/R/BiocFileCache/2969246b12_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 22:19:24.552885 loading file /github/home/.cache/R/BiocFileCache/295ea19ac5_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 23:00:59.756597 loading file /github/home/.cache/R/BiocFileCache/2966a8bc07_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/RtmpijtU1U/Br2719/tissue_positions.csv"
+#> [1] "/tmp/RtmpRFXf8q/Br2719/tissue_positions.csv"
 prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/RtmpijtU1U/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpijtU1U/Br2719/scalefactors_json.json" 
+#> [1] "/tmp/RtmpRFXf8q/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/RtmpRFXf8q/Br2719/scalefactors_json.json" 
 
 ########################################################################
 #   Add array coordinates
diff --git a/reference/add_overlap_info.html b/reference/add_overlap_info.html
index 8cb94fe..1dc5015 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 22:19:38.470479 loading file /github/home/.cache/R/BiocFileCache/29568707510_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 23:01:13.124129 loading file /github/home/.cache/R/BiocFileCache/29632475d0e_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 f7e5157..5ad5bcd 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 22:19:43.305967 loading file /github/home/.cache/R/BiocFileCache/29538a254d3_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 23:01:17.581873 loading file /github/home/.cache/R/BiocFileCache/2969246b12_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 22:19:45.92674 loading file /github/home/.cache/R/BiocFileCache/295ea19ac5_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 23:01:20.119519 loading file /github/home/.cache/R/BiocFileCache/2966a8bc07_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/RtmpijtU1U/Br2719/tissue_positions.csv"
+#> [1] "/tmp/RtmpRFXf8q/Br2719/tissue_positions.csv"
 prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/RtmpijtU1U/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpijtU1U/Br2719/scalefactors_json.json" 
+#> [1] "/tmp/RtmpRFXf8q/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/RtmpRFXf8q/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 22:19:51.983376 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
-#> 2024-07-26 22:19:59.000556 read10xVisiumAnalysis: reading analysis output from SpaceRanger
-#> 2024-07-26 22:19:59.347873 add10xVisiumAnalysis: adding analysis output from SpaceRanger
-#> 2024-07-26 22:19:59.680789 rtracklayer::import: reading the reference GTF file
-#> 2024-07-26 22:20:28.254342 adding gene information to the SPE object
+#> 2024-07-26 23:01:26.171491 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
+#> 2024-07-26 23:01:32.886996 read10xVisiumAnalysis: reading analysis output from SpaceRanger
+#> 2024-07-26 23:01:33.19475 add10xVisiumAnalysis: adding analysis output from SpaceRanger
+#> 2024-07-26 23:01:33.503458 rtracklayer::import: reading the reference GTF file
+#> 2024-07-26 23:02:02.232339 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 22:20:28.485601 adding information used by spatialLIBD
+#> 2024-07-26 23:02:02.459407 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 dab0e99..03e5574 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 22:20:32.094462 loading file /github/home/.cache/R/BiocFileCache/29538a254d3_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 23:02:06.038543 loading file /github/home/.cache/R/BiocFileCache/2969246b12_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 22:20:34.595874 loading file /github/home/.cache/R/BiocFileCache/295ea19ac5_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 23:02:08.50931 loading file /github/home/.cache/R/BiocFileCache/2966a8bc07_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/RtmpijtU1U/Br2719/tissue_positions.csv"
+#> [1] "/tmp/RtmpRFXf8q/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 5ba3fb6..41b65ca 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 22:20:43.368148 loading file /github/home/.cache/R/BiocFileCache/29538a254d3_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 23:02:17.047145 loading file /github/home/.cache/R/BiocFileCache/2969246b12_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 22:20:45.828853 loading file /github/home/.cache/R/BiocFileCache/295ea19ac5_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 23:02:19.528627 loading file /github/home/.cache/R/BiocFileCache/2966a8bc07_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/RtmpijtU1U/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpijtU1U/Br2719/scalefactors_json.json" 
+#> [1] "/tmp/RtmpRFXf8q/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/RtmpRFXf8q/Br2719/scalefactors_json.json" 
 
    
     
    
   
    
diff --git a/reference/rescale_fiji_inputs.html b/reference/rescale_fiji_inputs.html
index bc4b95f..e0a550a 100644
--- a/reference/rescale_fiji_inputs.html
+++ b/reference/rescale_fiji_inputs.html
@@ -136,7 +136,7 @@ 
    Examples
    
     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
     exdir = sr_dir
 )
-#> 2024-07-26 22:20:54.560397 loading file /github/home/.cache/R/BiocFileCache/29538a254d3_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 23:02:28.136843 loading file /github/home/.cache/R/BiocFileCache/2969246b12_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 22:20:57.07391 loading file /github/home/.cache/R/BiocFileCache/295ea19ac5_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 23:02:30.601578 loading file /github/home/.cache/R/BiocFileCache/2966a8bc07_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] "file2fce2e7aff05"                         
-#> [16] "file2fce31f65b43"                         
-#> [17] "file2fce360c7c08"                         
-#> [18] "file2fce4bfff4a3"                         
-#> [19] "file2fce4c3e127c"                         
-#> [20] "file2fce78d2b437"                         
+#> [15] "file2fd0152699d1"                         
+#> [16] "file2fd017f73280"                         
+#> [17] "file2fd025450c82"                         
+#> [18] "file2fd02e1b8484"                         
+#> [19] "file2fd038128303"                         
+#> [20] "file2fd077de19a2"
diff --git a/reference/spe_to_seurat.html b/reference/spe_to_seurat.html index 464601d..372fca9 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 22:21:05.595099 loading file /github/home/.cache/R/BiocFileCache/d5e26c460e8_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-07-26 23:02:39.186714 loading file /github/home/.cache/R/BiocFileCache/d5e415ba108_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 22:21:15.907325 loading file /github/home/.cache/R/BiocFileCache/29568707510_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 23:02:49.435264 loading file /github/home/.cache/R/BiocFileCache/29632475d0e_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_