diff --git a/R/fetch_data.R b/R/fetch_data.R index 97a75a8b..635a759a 100644 --- a/R/fetch_data.R +++ b/R/fetch_data.R @@ -103,7 +103,15 @@ fetch_data <- "Visium_SPG_AD_Visium_wholegenome_modeling_results", "visiumStitched_brain_spe", "visiumStitched_brain_spaceranger", - "visiumStitched_brain_Fiji_out" + "visiumStitched_brain_Fiji_out", + "LFF_spatial_ERC_SRT", + "LFF_spatial_ERC_SRT_pseudobulk", + "LFF_spatial_ERC_SRT_modeling_results", + "LFF_spatial_ERC_snRNAseq", + "LFF_spatial_ERC_snRNAseq_pseudobulk_broad", + "LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster", + "LFF_spatial_ERC_snRNAseq_modeling_results_broad", + "LFF_spatial_ERC_snRNAseq_modeling_results_subcluster" ), destdir = tempdir(), eh = ExperimentHub::ExperimentHub(), @@ -286,6 +294,70 @@ fetch_data <- file_name <- "visiumStitched_brain_fiji_out.zip" url <- "https://www.dropbox.com/scl/fi/bevo52e96f2kdwllf8dkk/visiumStitched_brain_fiji_out.zip?rlkey=ptwal8f5zxakzejwd0oqw0lhj&dl=1" + } else if (type == "LFF_spatial_ERC_SRT") { + tag <- "LFF_spatial_ERC" + hub_title <- type + + ## While EH is not set-up + file_name <- "spe_ERC_annotated.zip" + url <- + "https://www.dropbox.com/scl/fi/jrfc2tllppk52yqm1zyb3/spe_ERC_annotated.zip?rlkey=shi4pn3acf916dtscin32zjsn&dl=1" + } else if (type == "LFF_spatial_ERC_SRT_pseudobulk") { + tag <- "LFF_spatial_ERC" + hub_title <- type + + ## While EH is not set-up + file_name <- "spe_pseudobulk-SpD.rds" + url <- + "https://www.dropbox.com/scl/fi/2cl002smtcl37vaawodil/spe_pseudobulk-SpD.rds?rlkey=6igag1uggpg7h70ruucbl7leb&dl=1" + }else if (type == "LFF_spatial_ERC_SRT_modeling_results") { + tag <- "LFF_spatial_ERC" + hub_title <- type + + ## While EH is not set-up + file_name <- "modeling_results-SpD.rds" + url <- + "https://www.dropbox.com/scl/fi/4emtnag2x2usb8t4njvb9/modeling_results-SpD.rds?rlkey=d2qr82rz6uargnthkkahrs7e1&dl=1" + } else if (type == "LFF_spatial_ERC_snRNAseq") { + tag <- "LFF_spatial_ERC" + hub_title <- type + + ## While EH is not set-up + file_name <- "sce_ERC_subcluster.zip" + url <- + "https://www.dropbox.com/scl/fi/plekynuzpb22ii08pcn4j/sce_ERC_subcluster.zip?rlkey=bsgqc5dx4o0memidhs943qdhx&dl=1" + } else if (type == "LFF_spatial_ERC_snRNAseq_pseudobulk_broad") { + tag <- "LFF_spatial_ERC" + hub_title <- type + + ## While EH is not set-up + file_name <- "sce_subcluster_pseudobulk-cell_type_broad.rds" + url <- + "https://www.dropbox.com/scl/fi/supihrwunx99ldzztzecm/sce_subcluster_pseudobulk-cell_type_broad.rds?rlkey=uy7zmoifjhetfglrav4i2j0ns&dl=1" + } else if (type == "LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster") { + tag <- "LFF_spatial_ERC" + hub_title <- type + + ## While EH is not set-up + file_name <- "sce_subcluster_pseudobulk-cell_type_anno.rds" + url <- + "https://www.dropbox.com/scl/fi/c1n4i90k5pny7lij3gvxv/sce_subcluster_pseudobulk-cell_type_anno.rds?rlkey=v3kyay0p2i3h24u7c8fx2dn7u&dl=1" + } else if (type == "LFF_spatial_ERC_snRNAseq_modeling_results_broad") { + tag <- "LFF_spatial_ERC" + hub_title <- type + + ## While EH is not set-up + file_name <- "sce_subcluster_pseudobulk-cell_type_broad.rds" + url <- + "https://www.dropbox.com/scl/fi/eu9z1qp3gx5verdadwpyu/sce_subcluster_modeling_results-cell_type_broad.rds?rlkey=lwd66c7x5vdqeky431unanp45&dl=1" + } else if (type == "LFF_spatial_ERC_snRNAseq_modeling_results_subcluster") { + tag <- "LFF_spatial_ERC" + hub_title <- type + + ## While EH is not set-up + file_name <- "sce_subcluster_pseudobulk-cell_type_anno.rds" + url <- + "https://www.dropbox.com/scl/fi/y42pv7k02luvznwqii2rm/sce_subcluster_modeling_results-cell_type_anno.rds?rlkey=17c0ybowjpejdxc71tuxlcfna&dl=1" } file_path <- file.path(destdir, file_name) diff --git a/inst/extdata/metadata_LFF_spatial_ERC.csv b/inst/extdata/metadata_LFF_spatial_ERC.csv new file mode 100644 index 00000000..18befc8d --- /dev/null +++ b/inst/extdata/metadata_LFF_spatial_ERC.csv @@ -0,0 +1,9 @@ +Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath,Tags +LFF_spatial_ERC_SRT,SpatialExperiment object at the spot-level for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (n = 31) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SpatialExperiment,FilePath,spatialLIBD/spatialLIBD_files/spe_ERC_annotated.zip,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD +LFF_spatial_ERC_SRT_pseudobulk,Pseudo-bulked SingleCellExperiment object (SpatialExperiment object without spatial data) at the Sp09D spatial domain resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (n = 31) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SingleCellExperiment,Rds,spatialLIBD/spatialLIBD_files/spe_pseudobulk-SpD.rds,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD +LFF_spatial_ERC_SRT_modeling_results,List of modeling results at the Sp09D spatial domain resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Rds,spatialLIBD/spatialLIBD_files/modeling_results-SpD.rds,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD +LFF_spatial_ERC_snRNAseq,"SingleCellExperiment object for the LFF_spatial_ERC human brain (ERC) single nucleus transcriptomics data (snRNA-seq, n = 31) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SingleCellExperiment,FilePath,spatialLIBD/spatialLIBD_files/sce_ERC_subcluster.zip,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD +LFF_spatial_ERC_snRNAseq_pseudobulk_broad,"Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (n = 31) at 9 broad cell type resolution, from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SingleCellExperiment,Rds,spatialLIBD/spatialLIBD_files/sce_pseudo_DGE-cell_type_broad.RDS,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD +LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster,"Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (n = 31) at 38 subcluster resolution, from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SingleCellExperiment,Rds,spatialLIBD/spatialLIBD_files/sce_pseudo_DGE-cell_type_anno.RDS,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD +LFF_spatial_ERC_snRNAseq_modeling_results_broad,List of modeling results at the 9 broad cell type resolution for the LFF_spatial_ERC human brain (ERC) for snRNA-seq (n = 31) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Rds,spatialLIBD/spatialLIBD_files/sce_subcluster_pseudobulk-cell_type_broad.rds,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD +LFF_spatial_ERC_snRNAseq_modeling_results_subcluster,List of modeling results at the 38 subcluster resolution for the LFF_spatial_ERC human brain (ERC) for snRNA-seq (n = 31) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Rds,spatialLIBD/spatialLIBD_files/sce_subcluster_modeling_results-cell_type_anno.rds,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD \ No newline at end of file diff --git a/inst/scripts/make-metadata_LFF_spatial_ERC.R b/inst/scripts/make-metadata_LFF_spatial_ERC.R new file mode 100644 index 00000000..c74854cf --- /dev/null +++ b/inst/scripts/make-metadata_LFF_spatial_ERC.R @@ -0,0 +1,236 @@ +library("here") +library("sessioninfo") + + +outdir <- "spatialLIBD_files" +pkgname <- "spatialLIBD" + + +meta <- data.frame( + Title = c( + "LFF_spatial_ERC_SRT", + "LFF_spatial_ERC_SRT_pseudobulk", + "LFF_spatial_ERC_SRT_modeling_results", + "LFF_spatial_ERC_snRNAseq", + "LFF_spatial_ERC_snRNAseq_pseudobulk_broad", + "LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster", + "LFF_spatial_ERC_snRNAseq_modeling_results_broad", + "LFF_spatial_ERC_snRNAseq_modeling_results_subcluster" + ), + Description = c( + "SpatialExperiment object at the spot-level for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (n = 31) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.", + "Pseudo-bulked SingleCellExperiment object (SpatialExperiment object without spatial data) at the Sp09D spatial domain resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (n = 31) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.", + "List of modeling results at the Sp09D spatial domain resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.", + "SingleCellExperiment object for the LFF_spatial_ERC human brain (ERC) single nucleus transcriptomics data (snRNA-seq, n = 31) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.", + "Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (n = 31) at 9 broad cell type resolution, from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.", + "Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (n = 31) at 38 subcluster resolution, from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.", + "List of modeling results at the 9 broad cell type resolution for the LFF_spatial_ERC human brain (ERC) for snRNA-seq (n = 31) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.", + "List of modeling results at the 38 subcluster resolution for the LFF_spatial_ERC human brain (ERC) for snRNA-seq (n = 31) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package." + ), + BiocVersion = "3.17", + Genome = "GRCh38", + SourceType = "GTF", + SourceUrl = "https://bioconductor.org/packages/spatialLIBD", + SourceVersion = "Nov 20 2025", + Species = "Homo sapiens", + TaxonomyId = 9606, + Coordinate_1_based = TRUE, + DataProvider = "LIBD", + Maintainer = "Leonardo Collado-Torres ", + RDataClass = c( + "SpatialExperiment", + "SingleCellExperiment", + "list", + "SingleCellExperiment", + "SingleCellExperiment", + "SingleCellExperiment", + "list", + "list" + ), + DispatchClass = c("FilePath", "Rds", "Rds", "FilePath", "Rds", "Rds", "Rds", "Rds"), + RDataPath = file.path( + pkgname, + outdir, + c( + "spe_ERC_annotated.zip", + "spe_pseudobulk-SpD.rds", + "modeling_results-SpD.rds", + "sce_ERC_subcluster.zip", + "sce_subcluster_pseudobulk-cell_type_broad.rds", + "sce_subcluster_pseudobulk-cell_type_anno.rds", + "sce_subcluster_pseudobulk-cell_type_broad.rds", + "sce_subcluster_modeling_results-cell_type_anno.rds" + ) + ), + Tags = "Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD", + row.names = NULL, + stringsAsFactors = FALSE +) + +write.csv( + meta, + file = here::here("inst", "extdata", "metadata_LFF_spatial_ERC.csv"), + row.names = FALSE +) + +## Check +if (FALSE) { + AnnotationHubData::makeAnnotationHubMetadata(here::here(), fileName = "metadata_LFF_spatial_ERC.csv") +} + +## Reproducibility information +print("Reproducibility information:") +Sys.time() +proc.time() +options(width = 120) +session_info() + +# ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── +# setting value +# version R version 4.2.2 (2022-10-31) +# os macOS Ventura 13.0.1 +# system aarch64, darwin20 +# ui RStudio +# language (EN) +# collate en_US.UTF-8 +# ctype en_US.UTF-8 +# tz America/Mexico_City +# date 2023-02-13 +# rstudio 2022.12.0+353 Elsbeth Geranium (desktop) +# pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) +# +# ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── +# package * version date (UTC) lib source +# AnnotationDbi 1.60.0 2022-11-01 [1] Bioconductor +# AnnotationForge 1.40.0 2022-11-01 [1] Bioconductor +# AnnotationHub 3.6.0 2022-11-01 [1] Bioconductor +# AnnotationHubData 1.28.0 2022-11-01 [1] Bioconductor +# assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0) +# 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[1] CRAN (R 4.2.1) +# lubridate 1.9.1 2023-01-24 [1] CRAN (R 4.2.0) +# magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) +# Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.0) +# MatrixGenerics 1.10.0 2022-11-01 [1] Bioconductor +# matrixStats 0.63.0 2022-11-18 [1] CRAN (R 4.2.0) +# memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0) +# mime 0.12 2021-09-28 [1] CRAN (R 4.2.0) +# miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0) +# OrganismDbi 1.40.0 2022-11-01 [1] Bioconductor +# pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0) +# pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.2) +# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) +# pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.2) +# png 0.1-8 2022-11-29 [1] CRAN (R 4.2.0) +# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0) +# processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.0) +# profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.0) +# progress 1.2.2 2019-05-16 [1] CRAN (R 4.2.0) +# promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0) +# prompt 1.0.1 2022-03-01 [1] Github (gaborcsardi/prompt@7ef0f2e) +# ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.0) +# purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.0) +# R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) +# rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.2.0) +# RBGL 1.74.0 2022-11-01 [1] Bioconductor +# Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.2.0) +# RCurl 1.98-1.10 2023-01-27 [1] CRAN (R 4.2.0) +# remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0) +# restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.2.0) +# rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.0) +# rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0) +# rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.0) +# rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0) +# Rsamtools 2.14.0 2022-11-01 [1] Bioconductor +# RSQLite 2.2.20 2022-12-22 [1] CRAN (R 4.2.2) +# rsthemes 0.3.1 2022-03-01 [1] Github (gadenbuie/rsthemes@bbe73ca) +# rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0) +# rtracklayer 1.58.0 2022-11-01 [1] Bioconductor +# RUnit 0.4.32 2018-05-18 [1] CRAN (R 4.2.0) +# S4Vectors 0.36.1 2022-12-07 [1] Bioconductor +# sessioninfo * 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) +# shiny 1.7.4 2022-12-15 [1] CRAN (R 4.2.2) +# stringdist 0.9.10 2022-11-07 [1] CRAN (R 4.2.0) +# stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.0) +# stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.0) +# SummarizedExperiment 1.28.0 2022-11-01 [1] Bioconductor +# suncalc 0.5.1 2022-09-29 [1] CRAN (R 4.2.0) +# testthat * 3.1.6 2022-12-09 [1] CRAN (R 4.2.0) +# tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1) +# tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0) +# timechange 0.2.0 2023-01-11 [1] CRAN (R 4.2.0) +# urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0) +# usethis * 2.1.6 2022-05-25 [1] CRAN (R 4.2.0) +# utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0) +# vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.2.0) +# xfun 0.37 2023-01-31 [1] CRAN (R 4.2.0) +# XML 3.99-0.13 2022-12-04 [1] CRAN (R 4.2.0) +# xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0) +# xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0) +# XVector 0.38.0 2022-11-01 [1] Bioconductor +# yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0) +# zlibbioc 1.44.0 2022-11-01 [1] Bioconductor +# +# [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library +# +# ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── diff --git a/man/fetch_data.Rd b/man/fetch_data.Rd index 8f40a5b7..369a71c2 100644 --- a/man/fetch_data.Rd +++ b/man/fetch_data.Rd @@ -12,7 +12,14 @@ fetch_data( "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", "visiumStitched_brain_spe", - "visiumStitched_brain_spaceranger", "visiumStitched_brain_Fiji_out"), + "visiumStitched_brain_spaceranger", "visiumStitched_brain_Fiji_out", + + "LFF_spatial_ERC_SRT", "LFF_spatial_ERC_SRT_pseudobulk", + "LFF_spatial_ERC_SRT_modeling_results", "LFF_spatial_ERC_snRNAseq", + "LFF_spatial_ERC_snRNAseq_pseudobulk_broad", + "LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster", + "LFF_spatial_ERC_snRNAseq_modeling_results_broad", + "LFF_spatial_ERC_snRNAseq_modeling_results_subcluster"), destdir = tempdir(), eh = ExperimentHub::ExperimentHub(), bfc = BiocFileCache::BiocFileCache() diff --git a/tests/testthat/test-fetch_data.R b/tests/testthat/test-fetch_data.R new file mode 100644 index 00000000..8e27b4ae --- /dev/null +++ b/tests/testthat/test-fetch_data.R @@ -0,0 +1,46 @@ +test_that("multiplication works", { + expect_error(fetch_data(type = "BAD_TYPE")) +}) + + +## test ERC + +# ## SRT data +# spe_erc_path <- fetch_data(type = "LFF_spatial_ERC_SRT") +# spe_erc_path <- unzip(spe_erc_path, exdir = tempdir()) +# spe_erc <- HDF5Array::loadHDF5SummarizedExperiment( +# file.path(tempdir(), "spe_ERC_annotated") +# ) +# spe_erc +# dim: 30494 122202 +# lobstr::obj_size(spe_erc) 3.20 GB +# +# ## SCE data +# sce_erc_path <- fetch_data(type = "LFF_spatial_ERC_snRNAseq") +# sce_erc_path <- unzip(sce_erc_path, exdir = tempdir()) +# sce_erc <- HDF5Array::loadHDF5SummarizedExperiment( +# file.path(tempdir(), "sce_ERC_subcluster") +# ) +# sce_erc +# # dim: 38606 122004 +# # lobstr::obj_size(sce_erc) 258.20 MB +# +# +# erc_simple_types <- c("LFF_spatial_ERC_SRT_pseudobulk", +# "LFF_spatial_ERC_SRT_modeling_results", +# "LFF_spatial_ERC_snRNAseq_pseudobulk_broad", +# "LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster", +# "LFF_spatial_ERC_snRNAseq_modeling_results_broad", +# "LFF_spatial_ERC_snRNAseq_modeling_results_subcluster") +# +# names(erc_simple_types) <- erc_simple_types +# erc_data_test <- purrr::map(erc_simple_types, fetch_data) +# +# purrr::map_int(erc_data_test, length) +# purrr::map_chr(erc_data_test, class) +# LFF_spatial_ERC_SRT_pseudobulk LFF_spatial_ERC_SRT_modeling_results +# "SpatialExperiment" "list" +# LFF_spatial_ERC_snRNAseq_pseudobulk_broad LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster +# "SingleCellExperiment" "SingleCellExperiment" +# LFF_spatial_ERC_snRNAseq_modeling_results_broad LFF_spatial_ERC_snRNAseq_modeling_results_subcluster +# "list" "list"