Change from LS_visiumStitched to visiumStitched_brain

Co-authored-by: Nick Eagles <[email protected]>

R/fetch_data.R

@@ -100,9 +100,9 @@ fetch_data <-
         "Visium_SPG_AD_Visium_targeted_spe",
         "Visium_SPG_AD_Visium_wholegenome_pseudobulk_spe",
         "Visium_SPG_AD_Visium_wholegenome_modeling_results",
-        "Visium_LS_spe",
-        "Visium_LS_spaceranger",
-        "Visium_LS_ImageJ_out"
+        "visiumStitched_brain_spe",
+        "visiumStitched_brain_spaceranger",
+        "visiumStitched_brain_ImageJ_out"
     ),
     destdir = tempdir(),
     eh = ExperimentHub::ExperimentHub(),
@@ -266,25 +266,25 @@ fetch_data <-
             hub_title <- type
 
             ## While EH is not set-up
-            file_name <- "Visium_LS_spe.rds"
+            file_name <- "visiumStitched_brain_spe.rds"
             url <-
-                "https://www.dropbox.com/scl/fi/9re464y6qaojx3r94nq5u/Visium_LS_spe.rds?rlkey=nq6a82u23xuu9hohr86oodwdi&dl=1"
-        } else if (type == "Visium_LS_spaceranger") {
+                "https://www.dropbox.com/scl/fi/9re464y6qaojx3r94nq5u/visiumStitched_brain_spe.rds?rlkey=nq6a82u23xuu9hohr86oodwdi&dl=1"
+        } else if (type == "visiumStitched_brain_spaceranger") {
             tag <- "VisiumLS_Visium_stitched_spatialLIBD"
             hub_title <- type
 
             ## While EH is not set-up
-            file_name <- "Visium_LS_spaceranger.zip"
+            file_name <- "visiumStitched_brain_spaceranger.zip"
             url <-
-                "https://www.dropbox.com/scl/fi/5jdoaukvhq3v7lk19228y/Visium_LS_spaceranger.zip?rlkey=bdgjc6mgy1ierdad6h6v5g29c&dl=1"
-        } else if (type == "Visium_LS_ImageJ_out") {
+                "https://www.dropbox.com/scl/fi/5jdoaukvhq3v7lk19228y/visiumStitched_brain_spaceranger.zip?rlkey=bdgjc6mgy1ierdad6h6v5g29c&dl=1"
+        } else if (type == "visiumStitched_brain_ImageJ_out") {
             tag <- "VisiumLS_Visium_stitched_spatialLIBD"
             hub_title <- type
 
             ## While EH is not set-up
-            file_name <- "Visium_LS_imagej_out.zip"
+            file_name <- "visiumStitched_brain_imagej_out.zip"
             url <-
-                "https://www.dropbox.com/scl/fi/bevo52e96f2kdwllf8dkk/Visium_LS_imagej_out.zip?rlkey=ptwal8f5zxakzejwd0oqw0lhj&dl=1"
+                "https://www.dropbox.com/scl/fi/bevo52e96f2kdwllf8dkk/visiumStitched_brain_imagej_out.zip?rlkey=ptwal8f5zxakzejwd0oqw0lhj&dl=1"
         }
 
         file_path <- file.path(destdir, file_name)

inst/extdata/metadata_visiumStitched_brain.csv

@@ -0,0 +1,4 @@
+Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath,Tags
+visiumStitched_brain_spe,SpatialExperiment object at the spot-level for the spatially stitched human brain spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.19,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <[email protected]>,SpatialExperiment,Rds,spatialLIBD/spatialLIBD_files/visiumStitched_brain_spe.rds,visiumStitched_brain_spatialLIBD
+visiumStitched_brain_spaceranger,Spaceranger outputs for the spatially stitched human brain (spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Can be used with visiumStitched::build_spe() to construct a SpatialExperiment.,3.19,GRCh38,Zip,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <[email protected]>,list,Zip,spatialLIBD/spatialLIBD_files/visiumStitched_brain_spaceranger.zip,visiumStitched_brain_spatialLIBD
+visiumStitched_brain_ImageJ_out,Stitched PNG image and XML file from aligning human brain spatial transcriptomics data (n = 3) in ImageJ. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package.,3.19,GRCh38,Zip,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <[email protected]>,list,Zip,spatialLIBD/spatialLIBD_files/visiumStitched_brain_imagej_out.zip,visiumStitched_brain_spatialLIBD

inst/scripts/make-metadata_Visium_LS.R → inst/scripts/make-metadata_visiumStitched_brain.R

@@ -6,11 +6,11 @@ outdir <- "spatialLIBD_files"
 pkgname <- "spatialLIBD"
 
 meta <- tibble(
-    Title = c("Visium_LS_spe", "Visium_LS_spaceranger", "Visium_LS_ImageJ_out"),
+    Title = c("visiumStitched_brain_spe", "visiumStitched_brain_spaceranger", "visiumStitched_brain_ImageJ_out"),
     Description = c(
-        "SpatialExperiment object at the spot-level for the spatially stitched lateral septum human brain (LS) spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
-        "Spaceranger outputs for the spatially stitched lateral septum human brain (LS) spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Can be used with visiumStitched::build_spe() to construct a SpatialExperiment.",
-        "Stitched PNG image and XML file from aligning lateral septum human brain (LS) spatial transcriptomics data (n = 3) in ImageJ. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package."
+        "SpatialExperiment object at the spot-level for the spatially stitched human brain spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",
+        "Spaceranger outputs for the spatially stitched human brain (spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Can be used with visiumStitched::build_spe() to construct a SpatialExperiment.",
+        "Stitched PNG image and XML file from aligning human brain spatial transcriptomics data (n = 3) in ImageJ. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package."
     ),
     BiocVersion = "3.19",
     Genome = "GRCh38",
@@ -28,20 +28,20 @@ meta <- tibble(
         pkgname,
         outdir,
         c(
-            "Visium_LS_spe.rds", "Visium_LS_spaceranger.zip",
-            "Visium_LS_imagej_out.zip"
+            "visiumStitched_brain_spe.rds", "visiumStitched_brain_spaceranger.zip",
+            "visiumStitched_brain_imagej_out.zip"
         )
     ),
-    Tags = "VisiumLS_Visium_stitched_spatialLIBD"
+    Tags = "visiumStitched_brain_spatialLIBD"
 )
 
-write_csv(meta, here("inst", "extdata", "metadata_Visium_LS.csv"))
+write_csv(meta, here("inst", "extdata", "metadata_visiumStitched_brain.csv"))
 
 ## Check interactively
 if (FALSE) {
     AnnotationHubData::makeAnnotationHubMetadata(
         here(),
-        fileName = "metadata_Visium_LS.csv"
+        fileName = "metadata_visiumStitched_brain.csv"
     )
 }