Preparing Experiment Information#> # A tibble: 3 × 3
#> group capture_area spaceranger_dir
#> <chr> <chr> <chr>
-#> 1 Br2719 V13B23-283_A1 /tmp/Rtmp8BzNaV/V13B23-283_A1/outs/spatial
-#> 2 Br2719 V13B23-283_C1 /tmp/Rtmp8BzNaV/V13B23-283_C1/outs/spatial
-#> 3 Br2719 V13B23-283_D1 /tmp/Rtmp8BzNaV/V13B23-283_D1/outs/spatial
+#> 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
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/Rtmp8BzNaV/V1… 1.00 0.0825
-#> 2 Br2719 V13B23-283_C1 /tmp/Rtmp8BzNaV/V1… 1.00 0.0825
-#> 3 Br2719 V13B23-283_D1 /tmp/Rtmp8BzNaV/V1… 1 0.0825
+#> 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
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 18:34:36.534866 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:35:40.787131 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_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/Rtmp8BzNaV/V1… 1.00 0.0825
-#> 2 Br2719 V13B23-283_C1 /tmp/Rtmp8BzNaV/V1… 1.00 0.0825
-#> 3 Br2719 V13B23-283_D1 /tmp/Rtmp8BzNaV/V1… 1 0.0825
+#> 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
#> # 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/Rtmp8BzNaV/Br2719/tissue_positions.csv"
+#> [1] "/tmp/RtmpzaGKBG/Br2719/tissue_positions.csv"
prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/Rtmp8BzNaV/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/Rtmp8BzNaV/Br2719/scalefactors_json.json"
+#> [1] "/tmp/RtmpzaGKBG/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/RtmpzaGKBG/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 18:34:39.689923 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
-#> 2024-07-26 18:34:46.643242 read10xVisiumAnalysis: reading analysis output from SpaceRanger
-#> 2024-07-26 18:34:47.06622 add10xVisiumAnalysis: adding analysis output from SpaceRanger
-#> 2024-07-26 18:34:47.427486 rtracklayer::import: reading the reference GTF file
-#> 2024-07-26 18:35:18.798724 adding gene information to the SPE object
+#> 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
#> 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 18:35:19.02729 adding information used by spatialLIBD
+#> 2024-07-26 18:36:22.997012 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 18:35:28.329636 loading file /github/home/.cache/R/BiocFileCache/2ab7f5916f3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:36:31.772382 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_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)
@@ -554,8 +554,17 @@ Downstream applicationsk = 2
:
-## PRECAST k = 2 clusters
-vis_clus(spe_norm, clustervar = "precast_k2", is_stitched = TRUE)
+## PRECAST k = 2 clusters with our manually chosen colors
+vis_clus(
+ spe_norm,
+ clustervar = "precast_k2",
+ is_stitched = TRUE,
+ colors = c(
+ "1" = "gold",
+ "2" = "darkblue",
+ "NA" = "white"
+ )
+)
We can see that these two spatial clusters are differentiating the
white vs the gray matter based on the white matter marker genes we previously
@@ -568,7 +577,7 @@ Downstream applicationsvars[grep("precast", vars)]
#> [1] "precast_k2" "precast_k4" "precast_k8"
-## PRECAST k = 4 clusters
+## PRECAST k = 4 clusters with default cluster colors
vis_clus(spe_norm, clustervar = "precast_k4", is_stitched = TRUE)
The biological interpretation of these spatial clusters would need
@@ -680,9 +689,9 @@
Reproducibilitylibrary("knitr")
knit("visiumStitched.Rmd", tangle = TRUE)
Date the vignette was generated.
-#> [1] "2024-07-26 18:35:35 UTC"
+#> [1] "2024-07-26 18:36:39 UTC"
Wallclock time spent generating the vignette.
-#> Time difference of 1.487 mins
+#> Time difference of 1.458 mins
R session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
diff --git a/articles/visiumStitched_files/figure-html/precast_k2-1.png b/articles/visiumStitched_files/figure-html/precast_k2-1.png
index 062449c..ca5ebc0 100644
Binary files a/articles/visiumStitched_files/figure-html/precast_k2-1.png and b/articles/visiumStitched_files/figure-html/precast_k2-1.png differ
diff --git a/pkgdown.yml b/pkgdown.yml
index c9b8fb7..2f47c31 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: 2024-07-26T18:31Z
+last_built: 2024-07-26T18:32Z
diff --git a/reference/add_array_coords.html b/reference/add_array_coords.html
index b112e41..18bd0a1 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 18:31:59.299002 loading file /github/home/.cache/R/BiocFileCache/2ab7f5916f3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:33:11.689703 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_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 18:32:03.990414 loading file /github/home/.cache/R/BiocFileCache/2ab2c5cf8fa_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:33:15.777896 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
sample_info$spaceranger_dir <- file.path(
sr_dir, sample_info$capture_area, "outs", "spatial"
)
@@ -152,7 +152,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
exdir = fiji_dir
)
-#> 2024-07-26 18:32:06.745275 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:33:18.010393 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
sample_info$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/RtmpJXz24Y/Br2719/tissue_positions.csv"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_positions.csv"
prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/RtmpJXz24Y/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpJXz24Y/Br2719/scalefactors_json.json"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/Rtmp4mylSN/Br2719/scalefactors_json.json"
########################################################################
# Add array coordinates
diff --git a/reference/add_overlap_info.html b/reference/add_overlap_info.html
index fb38033..301a874 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 18:32:21.012287 loading file /github/home/.cache/R/BiocFileCache/2ab7f5916f3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:33:31.371027 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_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 106f19e..536097a 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 18:32:26.180631 loading file /github/home/.cache/R/BiocFileCache/2ab2c5cf8fa_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:33:35.64846 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
sample_info$spaceranger_dir <- file.path(
sr_dir, sample_info$capture_area, "outs", "spatial"
)
@@ -160,7 +160,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
exdir = fiji_dir
)
-#> 2024-07-26 18:32:29.036763 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:33:38.17873 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
sample_info$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/RtmpJXz24Y/Br2719/tissue_positions.csv"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_positions.csv"
prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/RtmpJXz24Y/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpJXz24Y/Br2719/scalefactors_json.json"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/Rtmp4mylSN/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 18:32:34.926612 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
-#> 2024-07-26 18:32:41.075502 read10xVisiumAnalysis: reading analysis output from SpaceRanger
-#> 2024-07-26 18:32:41.475474 add10xVisiumAnalysis: adding analysis output from SpaceRanger
-#> 2024-07-26 18:32:41.79351 rtracklayer::import: reading the reference GTF file
-#> 2024-07-26 18:33:10.396432 adding gene information to the SPE object
+#> 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
#> 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 18:33:10.628042 adding information used by spatialLIBD
+#> 2024-07-26 18:34:19.614623 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 c878fb5..174c5c6 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 18:33:14.80691 loading file /github/home/.cache/R/BiocFileCache/2ab2c5cf8fa_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:34:23.176996 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
sample_info$spaceranger_dir <- file.path(
sr_dir, sample_info$capture_area, "outs", "spatial"
)
@@ -122,7 +122,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
exdir = fiji_dir
)
-#> 2024-07-26 18:33:17.531123 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:34:25.562983 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
sample_info$fiji_image_path <- temp[grep("png$", temp)]
@@ -132,7 +132,7 @@ Examples
spe_input_dir <- tempdir()
out_file <- prep_fiji_coords(sample_info, out_dir = spe_input_dir)
out_file
-#> [1] "/tmp/RtmpJXz24Y/Br2719/tissue_positions.csv"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_positions.csv"
# A file of spatial coordinates for the stitched Br2719 was produced
readr::read_csv(out_file)
diff --git a/reference/prep_fiji_image.html b/reference/prep_fiji_image.html
index bf5aea4..03c135c 100644
--- a/reference/prep_fiji_image.html
+++ b/reference/prep_fiji_image.html
@@ -119,7 +119,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
exdir = sr_dir
)
-#> 2024-07-26 18:33:26.770156 loading file /github/home/.cache/R/BiocFileCache/2ab2c5cf8fa_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:34:34.360621 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
sample_info$spaceranger_dir <- file.path(
sr_dir, sample_info$capture_area, "outs", "spatial"
)
@@ -130,7 +130,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
exdir = fiji_dir
)
-#> 2024-07-26 18:33:29.546679 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:34:36.775245 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
sample_info$fiji_image_path <- temp[grep("png$", temp)]
@@ -194,8 +194,8 @@ Examples
# In total, an image and scalefactors were written
out_paths
-#> [1] "/tmp/RtmpJXz24Y/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpJXz24Y/Br2719/scalefactors_json.json"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/Rtmp4mylSN/Br2719/scalefactors_json.json"
diff --git a/reference/rescale_fiji_inputs.html b/reference/rescale_fiji_inputs.html
index bc5c729..a1e88b2 100644
--- a/reference/rescale_fiji_inputs.html
+++ b/reference/rescale_fiji_inputs.html
@@ -136,7 +136,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
exdir = sr_dir
)
-#> 2024-07-26 18:33:39.082253 loading file /github/home/.cache/R/BiocFileCache/2ab2c5cf8fa_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:34:45.683137 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
sample_info$spaceranger_dir <- file.path(
sr_dir, sample_info$capture_area, "outs", "spatial"
)
@@ -147,7 +147,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
exdir = fiji_dir
)
-#> 2024-07-26 18:33:41.875736 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:34:48.090167 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
sample_info$fiji_image_path <- temp[grep("png$", temp)]
@@ -181,12 +181,12 @@ Examples
#> [12] "V13B23-283_D1"
#> [13] "V13B23-283_D1.png"
#> [14] "downlit"
-#> [15] "file2fe411e7d65c"
-#> [16] "file2fe438f7ba8f"
-#> [17] "file2fe43ea8f037"
-#> [18] "file2fe465caebf3"
-#> [19] "file2fe46b6d4b9e"
-#> [20] "file2fe47fed6d78"
+#> [15] "file2fe526234c6c"
+#> [16] "file2fe537e3e75"
+#> [17] "file2fe5486b0347"
+#> [18] "file2fe54de20e80"
+#> [19] "file2fe57fc3ec5"
+#> [20] "file2fe5b855f"
diff --git a/reference/spe_to_seurat.html b/reference/spe_to_seurat.html
index 040ecc2..721c970 100644
--- a/reference/spe_to_seurat.html
+++ b/reference/spe_to_seurat.html
@@ -112,7 +112,7 @@ Author
Examples
## Download some example data
spe <- spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
-#> 2024-07-26 18:33:48.929309 loading file /github/home/.cache/R/BiocFileCache/d7410d7ae43_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-07-26 18:34:54.769072 loading file /github/home/.cache/R/BiocFileCache/d74272cc73b_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
## Make the column names unique
colnames(spe) <- spatialLIBD::add_key(spe)$key
@@ -143,7 +143,7 @@ Examples
## Example with an stitched SPE object
spe_stitched <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 18:34:00.544698 loading file /github/home/.cache/R/BiocFileCache/2ab7f5916f3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:35:05.705695 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_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_
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/Rtmp8BzNaV/V1… 1.00 0.0825
-#> 2 Br2719 V13B23-283_C1 /tmp/Rtmp8BzNaV/V1… 1.00 0.0825
-#> 3 Br2719 V13B23-283_D1 /tmp/Rtmp8BzNaV/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 18:34:36.534866 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:35:40.787131 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_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)]
fiji_dir <- tempdir()
temp <- unzip(fetch_data("visiumStitched_brain_Fiji_out"), exdir = fiji_dir)
-#> 2024-07-26 18:34:36.534866 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:35:40.787131 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_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)]sample_info that
@@ -269,9 +269,9 @@ Before building the We can see that these two spatial clusters are differentiating the
white vs the gray matter based on the white matter marker genes we previously
@@ -568,7 +577,7 @@ The biological interpretation of these spatial clusters would need
@@ -680,9 +689,9 @@ Date the vignette was generated. Wallclock time spent generating the vignette.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/Rtmp8BzNaV/Br2719/tissue_positions.csv"
+#> [1] "/tmp/RtmpzaGKBG/Br2719/tissue_positions.csv"
prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/Rtmp8BzNaV/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/Rtmp8BzNaV/Br2719/scalefactors_json.json"
+#> [1] "/tmp/RtmpzaGKBG/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/RtmpzaGKBG/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 18:34:39.689923 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
-#> 2024-07-26 18:34:46.643242 read10xVisiumAnalysis: reading analysis output from SpaceRanger
-#> 2024-07-26 18:34:47.06622 add10xVisiumAnalysis: adding analysis output from SpaceRanger
-#> 2024-07-26 18:34:47.427486 rtracklayer::import: reading the reference GTF file
-#> 2024-07-26 18:35:18.798724 adding gene information to the SPE object
+#> 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
#> 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 18:35:19.02729 adding information used by spatialLIBD
+#> 2024-07-26 18:36:22.997012 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 18:35:28.329636 loading file /github/home/.cache/R/BiocFileCache/2ab7f5916f3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:36:31.772382 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_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)
@@ -554,8 +554,17 @@ :
Downstream applicationsk = 2
-
## PRECAST k = 2 clusters
-vis_clus(spe_norm, clustervar = "precast_k2", is_stitched = TRUE)## PRECAST k = 2 clusters with our manually chosen colors
+vis_clus(
+ spe_norm,
+ clustervar = "precast_k2",
+ is_stitched = TRUE,
+ colors = c(
+ "1" = "gold",
+ "2" = "darkblue",
+ "NA" = "white"
+ )
+)Downstream applicationsvars[grep("precast", vars)]
#> [1] "precast_k2" "precast_k4" "precast_k8"
-## PRECAST k = 4 clusters
+## PRECAST k = 4 clusters with default cluster colors
vis_clus(spe_norm, clustervar = "precast_k4", is_stitched = TRUE)
Reproducibilitylibrary("knitr")
knit("visiumStitched.Rmd", tangle = TRUE)
+#> [1] "2024-07-26 18:35:35 UTC"#> [1] "2024-07-26 18:36:39 UTC"
+#> Time difference of 1.487 mins#> Time difference of 1.458 minsR session information.#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
diff --git a/articles/visiumStitched_files/figure-html/precast_k2-1.png b/articles/visiumStitched_files/figure-html/precast_k2-1.png
index 062449c..ca5ebc0 100644
Binary files a/articles/visiumStitched_files/figure-html/precast_k2-1.png and b/articles/visiumStitched_files/figure-html/precast_k2-1.png differ
diff --git a/pkgdown.yml b/pkgdown.yml
index c9b8fb7..2f47c31 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: 2024-07-26T18:31Z
+last_built: 2024-07-26T18:32Z
diff --git a/reference/add_array_coords.html b/reference/add_array_coords.html
index b112e41..18bd0a1 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 18:31:59.299002 loading file /github/home/.cache/R/BiocFileCache/2ab7f5916f3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:33:11.689703 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_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 18:32:03.990414 loading file /github/home/.cache/R/BiocFileCache/2ab2c5cf8fa_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:33:15.777896 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
sample_info$spaceranger_dir <- file.path(
sr_dir, sample_info$capture_area, "outs", "spatial"
)
@@ -152,7 +152,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
exdir = fiji_dir
)
-#> 2024-07-26 18:32:06.745275 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:33:18.010393 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
sample_info$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/RtmpJXz24Y/Br2719/tissue_positions.csv"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_positions.csv"
prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/RtmpJXz24Y/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpJXz24Y/Br2719/scalefactors_json.json"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/Rtmp4mylSN/Br2719/scalefactors_json.json"
########################################################################
# Add array coordinates
diff --git a/reference/add_overlap_info.html b/reference/add_overlap_info.html
index fb38033..301a874 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 18:32:21.012287 loading file /github/home/.cache/R/BiocFileCache/2ab7f5916f3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:33:31.371027 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_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 106f19e..536097a 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 18:32:26.180631 loading file /github/home/.cache/R/BiocFileCache/2ab2c5cf8fa_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:33:35.64846 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
sample_info$spaceranger_dir <- file.path(
sr_dir, sample_info$capture_area, "outs", "spatial"
)
@@ -160,7 +160,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
exdir = fiji_dir
)
-#> 2024-07-26 18:32:29.036763 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:33:38.17873 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
sample_info$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/RtmpJXz24Y/Br2719/tissue_positions.csv"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_positions.csv"
prep_fiji_image(sample_info, out_dir = spe_input_dir)
-#> [1] "/tmp/RtmpJXz24Y/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpJXz24Y/Br2719/scalefactors_json.json"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/Rtmp4mylSN/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 18:32:34.926612 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
-#> 2024-07-26 18:32:41.075502 read10xVisiumAnalysis: reading analysis output from SpaceRanger
-#> 2024-07-26 18:32:41.475474 add10xVisiumAnalysis: adding analysis output from SpaceRanger
-#> 2024-07-26 18:32:41.79351 rtracklayer::import: reading the reference GTF file
-#> 2024-07-26 18:33:10.396432 adding gene information to the SPE object
+#> 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
#> 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 18:33:10.628042 adding information used by spatialLIBD
+#> 2024-07-26 18:34:19.614623 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 c878fb5..174c5c6 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 18:33:14.80691 loading file /github/home/.cache/R/BiocFileCache/2ab2c5cf8fa_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:34:23.176996 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
sample_info$spaceranger_dir <- file.path(
sr_dir, sample_info$capture_area, "outs", "spatial"
)
@@ -122,7 +122,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
exdir = fiji_dir
)
-#> 2024-07-26 18:33:17.531123 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:34:25.562983 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
sample_info$fiji_image_path <- temp[grep("png$", temp)]
@@ -132,7 +132,7 @@ Examples
spe_input_dir <- tempdir()
out_file <- prep_fiji_coords(sample_info, out_dir = spe_input_dir)
out_file
-#> [1] "/tmp/RtmpJXz24Y/Br2719/tissue_positions.csv"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_positions.csv"
# A file of spatial coordinates for the stitched Br2719 was produced
readr::read_csv(out_file)
diff --git a/reference/prep_fiji_image.html b/reference/prep_fiji_image.html
index bf5aea4..03c135c 100644
--- a/reference/prep_fiji_image.html
+++ b/reference/prep_fiji_image.html
@@ -119,7 +119,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
exdir = sr_dir
)
-#> 2024-07-26 18:33:26.770156 loading file /github/home/.cache/R/BiocFileCache/2ab2c5cf8fa_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:34:34.360621 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
sample_info$spaceranger_dir <- file.path(
sr_dir, sample_info$capture_area, "outs", "spatial"
)
@@ -130,7 +130,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
exdir = fiji_dir
)
-#> 2024-07-26 18:33:29.546679 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:34:36.775245 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
sample_info$fiji_image_path <- temp[grep("png$", temp)]
@@ -194,8 +194,8 @@ Examples
# In total, an image and scalefactors were written
out_paths
-#> [1] "/tmp/RtmpJXz24Y/Br2719/tissue_lowres_image.png"
-#> [2] "/tmp/RtmpJXz24Y/Br2719/scalefactors_json.json"
+#> [1] "/tmp/Rtmp4mylSN/Br2719/tissue_lowres_image.png"
+#> [2] "/tmp/Rtmp4mylSN/Br2719/scalefactors_json.json"
Examples
spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
exdir = sr_dir
)
-#> 2024-07-26 18:33:39.082253 loading file /github/home/.cache/R/BiocFileCache/2ab2c5cf8fa_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
+#> 2024-07-26 18:34:45.683137 loading file /github/home/.cache/R/BiocFileCache/2aa161edeab_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
sample_info$spaceranger_dir <- file.path(
sr_dir, sample_info$capture_area, "outs", "spatial"
)
@@ -147,7 +147,7 @@ Examples
spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
exdir = fiji_dir
)
-#> 2024-07-26 18:33:41.875736 loading file /github/home/.cache/R/BiocFileCache/2ab384f9d1c_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
+#> 2024-07-26 18:34:48.090167 loading file /github/home/.cache/R/BiocFileCache/2aa366ab32d_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
sample_info$fiji_image_path <- temp[grep("png$", temp)]
@@ -181,12 +181,12 @@ Examples
#> [12] "V13B23-283_D1"
#> [13] "V13B23-283_D1.png"
#> [14] "downlit"
-#> [15] "file2fe411e7d65c"
-#> [16] "file2fe438f7ba8f"
-#> [17] "file2fe43ea8f037"
-#> [18] "file2fe465caebf3"
-#> [19] "file2fe46b6d4b9e"
-#> [20] "file2fe47fed6d78"
+#> [15] "file2fe526234c6c"
+#> [16] "file2fe537e3e75"
+#> [17] "file2fe5486b0347"
+#> [18] "file2fe54de20e80"
+#> [19] "file2fe57fc3ec5"
+#> [20] "file2fe5b855f"
Author
Examples
## Download some example data
spe <- spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
-#> 2024-07-26 18:33:48.929309 loading file /github/home/.cache/R/BiocFileCache/d7410d7ae43_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-07-26 18:34:54.769072 loading file /github/home/.cache/R/BiocFileCache/d74272cc73b_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
## Make the column names unique
colnames(spe) <- spatialLIBD::add_key(spe)$key
@@ -143,7 +143,7 @@ Examples
## Example with an stitched SPE object
spe_stitched <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
-#> 2024-07-26 18:34:00.544698 loading file /github/home/.cache/R/BiocFileCache/2ab7f5916f3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
+#> 2024-07-26 18:35:05.705695 loading file /github/home/.cache/R/BiocFileCache/2aa316c4122_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_