diff --git a/R/fetch_data.R b/R/fetch_data.R index 8f859e5b..06e17e09 100644 --- a/R/fetch_data.R +++ b/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) diff --git a/inst/extdata/metadata_Visium_LS.csv b/inst/extdata/metadata_Visium_LS.csv deleted file mode 100644 index 5b868cf7..00000000 --- a/inst/extdata/metadata_Visium_LS.csv +++ /dev/null @@ -1,4 +0,0 @@ -Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath,Tags -Visium_LS_spe,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.,3.19,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SpatialExperiment,Rds,spatialLIBD/spatialLIBD_files/Visium_LS_spe.rds,VisiumLS_Visium_stitched_spatialLIBD -Visium_LS_spaceranger,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.,3.19,GRCh38,Zip,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Zip,spatialLIBD/spatialLIBD_files/Visium_LS_spaceranger.zip,VisiumLS_Visium_stitched_spatialLIBD -Visium_LS_ImageJ_out,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.,3.19,GRCh38,Zip,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Zip,spatialLIBD/spatialLIBD_files/Visium_LS_imagej_out.zip,VisiumLS_Visium_stitched_spatialLIBD diff --git a/inst/extdata/metadata_visiumStitched_brain.csv b/inst/extdata/metadata_visiumStitched_brain.csv new file mode 100644 index 00000000..64af76ef --- /dev/null +++ b/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 ,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 ,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 ,list,Zip,spatialLIBD/spatialLIBD_files/visiumStitched_brain_imagej_out.zip,visiumStitched_brain_spatialLIBD diff --git a/inst/scripts/make-metadata_Visium_LS.R b/inst/scripts/make-metadata_visiumStitched_brain.R similarity index 89% rename from inst/scripts/make-metadata_Visium_LS.R rename to inst/scripts/make-metadata_visiumStitched_brain.R index 9fefe846..0f18ef34 100644 --- a/inst/scripts/make-metadata_Visium_LS.R +++ b/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" ) } diff --git a/man/fetch_data.Rd b/man/fetch_data.Rd index ac411d47..8a59b913 100644 --- a/man/fetch_data.Rd +++ b/man/fetch_data.Rd @@ -11,8 +11,8 @@ fetch_data( "spatialDLPFC_Visium_SPG", "spatialDLPFC_snRNAseq", "Visium_SPG_AD_Visium_wholegenome_spe", "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"), + "Visium_SPG_AD_Visium_wholegenome_modeling_results", "visiumStitched_brain_spe", + "visiumStitched_brain_spaceranger", "visiumStitched_brain_ImageJ_out"), destdir = tempdir(), eh = ExperimentHub::ExperimentHub(), bfc = BiocFileCache::BiocFileCache()