LieberInstitute
[BUG/clarification] Fetching pseudobulk data does not pass check_sce_layer
Describe the bug
fetch_data(spatialDLPFC_Visium_pseudobulk) provides a SpatialExperiment object which passes no checks out of 'check_spe', 'check_sce' or 'check_sce_layer'and no clear way to convert it for downstream applications
Provide a minimally reproducible example (reprex)
library(spatialLIBD) sce_layer <- spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_pseudobulk") check_spe(sce_layer) Error in check_spe(sce_layer) : all(c("sample_id", "image_id", "data", "scaleFactor") %in% colnames(imgData(spe))) is not TRUE check_sce(sce_layer) Error in check_sce(sce_layer) : "image" %in% names(metadata(sce)) is not TRUE check_sce_layer(sce_layer) Error in check_sce_layer(sce_layer) : all(variables %in% colnames(colData(sce_layer))) is not TRUE
Expected behavior
The pseudobulk data is eminently useful for the function 'sig_genes_extract_all' as an input for 'sce_layer', however the provided objects heavily impacts reproducibility so the remotely hosted object should be shifted to a SingleCellExperiment class that passes 'check_sce_layer' for consistency sake.
R Session Information
options(width = 120)
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] zellkonverter_1.16.0 spatialLIBD_1.18.0 SpatialExperiment_1.16.0 SingleCellExperiment_1.28.1
[5] SummarizedExperiment_1.36.0 Biobase_2.66.0 GenomicRanges_1.58.0 GenomeInfoDb_1.42.1
[9] IRanges_2.40.1 S4Vectors_0.44.0 BiocGenerics_0.52.0 MatrixGenerics_1.18.1
[13] matrixStats_1.5.0 ggplot2_3.5.1 edgeR_4.4.1 limma_3.62.2
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.8.9 magrittr_2.0.3 ggbeeswarm_0.7.2
[6] magick_2.8.5 BiocIO_1.16.0 fields_16.3 zlibbioc_1.52.0 vctrs_0.6.5
[11] memoise_2.0.1 config_0.3.2 Rsamtools_2.22.0 paletteer_1.6.0 RCurl_1.98-1.16
[16] benchmarkme_1.0.8 htmltools_0.5.8.1 S4Arrays_1.6.0 AnnotationHub_3.14.0 curl_6.1.0
[21] BiocNeighbors_2.0.1 SparseArray_1.6.1 sass_0.4.9 bslib_0.8.0 basilisk_1.18.0
[26] htmlwidgets_1.6.4 plotly_4.10.4 cachem_1.1.0 GenomicAlignments_1.42.0 mime_0.12
[31] lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3 rsvd_1.0.5 Matrix_1.7-2
[36] R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.13 shiny_1.10.0 digest_0.6.37
[41] colorspace_2.1-1 rematch2_2.1.2 AnnotationDbi_1.68.0 scater_1.34.0 irlba_2.3.5.1
[46] ExperimentHub_2.14.0 RSQLite_2.3.9 beachmat_2.22.0 filelock_1.0.3 httr_1.4.7
[51] abind_1.4-8 compiler_4.4.2 withr_3.0.2 bit64_4.6.0-1 doParallel_1.0.17
[56] attempt_0.3.1 BiocParallel_1.40.0 viridis_0.6.5 DBI_1.2.3 maps_3.4.2.1
[61] sessioninfo_1.2.2 rappdirs_0.3.3 DelayedArray_0.32.0 rjson_0.2.23 tools_4.4.2
[66] vipor_0.4.7 beeswarm_0.4.0 httpuv_1.6.15 glue_1.8.0 restfulr_0.0.15
[71] promises_1.3.2 grid_4.4.2 generics_0.1.3 gtable_0.3.6 tidyr_1.3.1
[76] data.table_1.16.4 BiocSingular_1.22.0 ScaledMatrix_1.14.0 XVector_0.46.0 stringr_1.5.1
[81] ggrepel_0.9.6 BiocVersion_3.20.0 foreach_1.5.2 pillar_1.10.1 spam_2.11-1
[86] later_1.4.1 benchmarkmeData_1.0.4 dplyr_1.1.4 BiocFileCache_2.14.0 lattice_0.22-6
[91] rtracklayer_1.66.0 bit_4.5.0.1 tidyselect_1.2.1 locfit_1.5-9.10 Biostrings_2.74.1
[96] scuttle_1.16.0 gridExtra_2.3 statmod_1.5.0 DT_0.33 stringi_1.8.4
[101] UCSC.utils_1.2.0 lazyeval_0.2.2 yaml_2.3.10 shinyWidgets_0.8.7 codetools_0.2-20
[106] tibble_3.2.1 BiocManager_1.30.25 cli_3.6.3 reticulate_1.40.0 xtable_1.8-4
[111] jquerylib_0.1.4 munsell_0.5.1 golem_0.5.1 Rcpp_1.0.14 dir.expiry_1.14.0
[116] dbplyr_2.5.0 png_0.1-8 XML_3.99-0.18 parallel_4.4.2 blob_1.2.4
[121] basilisk.utils_1.18.0 dotCall64_1.2 bitops_1.0-9 viridisLite_0.4.2 scales_1.3.0
[126] purrr_1.0.2 crayon_1.5.3 rlang_1.1.5 cowplot_1.1.3 KEGGREST_1.46.0
Indicate whether BiocManager::valid() returns TRUE.
- [+]
BiocManager::valid()isTRUE
Is the package installed via bioconda?
No, Biocmanager
Hi,
I couldn't reproduce your issue using the latest version of spatialLIBD:
devel* > sce_layer <- spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_pseudobulk")
snapshotDate(): 2024-10-24
adding rname 'https://www.dropbox.com/s/pbti4strsfk1m55/sce_pseudo_BayesSpace_k09.rds?dl=1'
|===========================================================================================| 100%
|===========================================================================================| 100%
2025-02-28 16:43:46.719131 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/9c5c633345f2_sce_pseudo_BayesSpace_k09.rds%3Fdl%3D1
devel* > sce_layer
class: SpatialExperiment
dim: 12225 268
metadata(1): PCA_var_explained
assays(2): counts logcounts
rownames(12225): ENSG00000237491 ENSG00000228794 ... ENSG00000198727 ENSG00000278817
rowData names(7): source type ... gene_type gene_search
colnames(268): Br2720_ant_Sp09D01 Br2720_mid_Sp09D01 ... Br8667_mid_Sp09D09
Br8667_post_Sp09D09
colData names(9): age BayesSpace ... subject BayesSpace_colors
reducedDimNames(3): PCA MDS runPCA
mainExpName: NULL
altExpNames(0):
spatialCoords names(0) :
imgData names(1): sample_id
devel > packageVersion("spatialLIBD")
[1] ‘1.19.8’
Do you still see this issue with the latest version if you install it with BiocManager::install("LieberInstitute/spatialLIBD")?
Best, Leo
