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LieberInstitute / spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app
http://LieberInstitute.github.io/spatialLIBD/
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[BUG] fetch_data(type = "spe") yields "Error: Other 'type' values are not supported." #47

Closed george-hall-ucl closed 11 months ago

george-hall-ucl commented 1 year ago

When I follow along with the tutorial in the README, I encounter an error early on. Running the first five lines in the Processed data section.

## Load the package
library("spatialLIBD")

## Download the spot-level data
spe <- fetch_data(type = "spe")

Yields:

  |======================================================================| 100%

snapshotDate(): 2020-10-27
Error: Other 'type' values are not supported. Please use either 'sce', 'sce_layer', 'modeling_results', 'sce_example' or 've'.

Expected behavior

Output given in README, i.e.:

## This is a SpatialExperiment object
spe
#> class: SpatialExperiment 
#> dim: 33538 47681 
#> metadata(0):
#> assays(2): counts logcounts
#> rownames(33538): ENSG00000243485 ENSG00000237613 ... ENSG00000277475
#>   ENSG00000268674
#> rowData names(9): source type ... gene_search is_top_hvg
#> colnames(47681): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
#>   TTGTTTCCATACAACT-1 TTGTTTGTGTAAATTC-1
#> colData names(69): sample_id Cluster ... array_row array_col
#> reducedDimNames(6): PCA TSNE_perplexity50 ... TSNE_perplexity80
#>   UMAP_neighbors15
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
#> imgData names(4): sample_id image_id data scaleFactor
R Session Information Please report the output of either `sessionInfo()` or `sessioninfo::session_info()` here. ```R options(width = 120) R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] shiny_1.7.1 spatialLIBD_1.2.1 [3] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0 [5] Biobase_2.50.0 GenomicRanges_1.42.0 [7] GenomeInfoDb_1.26.2 IRanges_2.24.1 [9] S4Vectors_0.28.1 BiocGenerics_0.36.0 [11] MatrixGenerics_1.2.1 matrixStats_0.61.0 loaded via a namespace (and not attached): [1] SpatialExperiment_1.0.0 ggbeeswarm_0.6.0 [3] colorspace_2.0-2 ellipsis_0.3.2 [5] benchmarkme_1.0.8 scuttle_1.0.4 [7] markdown_1.1 XVector_0.30.0 [9] fs_1.5.2 BiocNeighbors_1.8.2 [11] DT_0.17 bit64_4.0.5 [13] interactiveDisplayBase_1.28.0 AnnotationDbi_1.52.0 [15] Polychrome_1.5.1 golem_0.4.0 [17] fansi_0.5.0 codetools_0.2-18 [19] sparseMatrixStats_1.2.1 doParallel_1.0.16 [21] cachem_1.0.6 scater_1.18.6 [23] config_0.3.1 readbitmap_0.1.5 [25] spam_2.8-0 jsonlite_1.7.2 [27] dbplyr_2.1.1 png_0.1-7 [29] BiocManager_1.30.10 compiler_4.0.3 [31] httr_1.4.2 assertthat_0.2.1 [33] bmp_0.3 Matrix_1.5-3 [35] fastmap_1.1.0 lazyeval_0.2.2 [37] cli_3.6.0 later_1.3.0 [39] BiocSingular_1.6.0 htmltools_0.5.2 [41] tools_4.0.3 rsvd_1.0.3 [43] dotCall64_1.0-1 gtable_0.3.0 [45] glue_1.6.2 GenomeInfoDbData_1.2.4 [47] dplyr_1.1.0 maps_3.3.0 [49] rappdirs_0.3.3 Rcpp_1.0.7 [51] jquerylib_0.1.4 vctrs_0.5.2 [53] ExperimentHub_1.16.0 crosstalk_1.2.0 [55] iterators_1.0.13 DelayedMatrixStats_1.12.3 [57] xfun_0.39 stringr_1.4.0 [59] beachmat_2.6.4 mime_0.12 [61] lifecycle_1.0.3 irlba_2.3.5 [63] AnnotationHub_2.22.0 zlibbioc_1.36.0 [65] scales_1.2.1 promises_1.2.0.1 [67] RColorBrewer_1.1-2 fields_13.3 [69] yaml_2.2.1 curl_4.3.2 [71] memoise_2.0.0 gridExtra_2.3 [73] ggplot2_3.4.0 sass_0.4.0 [75] stringi_1.7.6 RSQLite_2.2.3 [77] BiocVersion_3.12.0 foreach_1.5.1 [79] tiff_0.1-11 BiocParallel_1.24.1 [81] attempt_0.3.1 benchmarkmeData_1.0.4 [83] rlang_1.0.6 pkgconfig_2.0.3 [85] bitops_1.0-7 fontawesome_0.5.1 [87] lattice_0.20-41 purrr_0.3.4 [89] htmlwidgets_1.5.4 cowplot_1.1.1 [91] bit_4.0.4 tidyselect_1.2.0 [93] magrittr_2.0.1 R6_2.5.1 [95] generics_0.1.3 DelayedArray_0.16.2 [97] DBI_1.1.1 withr_2.5.0 [99] pillar_1.8.1 scatterplot3d_0.3-41 [101] RCurl_1.98-1.2 tibble_3.1.8 [103] crayon_1.4.2 shinyWidgets_0.7.6 [105] utf8_1.2.2 BiocFileCache_1.14.0 [107] plotly_4.10.0 viridis_0.5.1 [109] jpeg_0.1-8.1 grid_4.0.3 [111] data.table_1.14.2 blob_1.2.1 [113] digest_0.6.29 xtable_1.8-4 [115] tidyr_1.2.0 httpuv_1.6.3 [117] munsell_0.5.0 beeswarm_0.3.1 [119] viridisLite_0.4.0 bslib_0.3.1 [121] vipor_0.4.5 sessioninfo_1.1.1 ``` Indicate whether `BiocManager::valid()` returns `TRUE`. - [ ] `BiocManager::valid()` is `TRUE` -- NO
lcolladotor commented 11 months ago

Hi @george-hall-ucl,

Sorry for the late response. I don't remember in which version of spatialLIBD we fixed that issue you are observing, but I can see that it all works with the latest version as you can see below.

devel > ## Load the package
devel > library("spatialLIBD")
Loading required package: SpatialExperiment
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts,
    colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs,
    colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2,
    colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges,
    colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars,
    colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse,
    rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs,
    rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs,
    rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles,
    rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates,
    rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max,
    which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To
    cite Bioconductor, see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

devel > 
devel > ## Download the spot-level data
devel > spe <- fetch_data(type = "spe")
  |=================================================================================| 100%

snapshotDate(): 2023-04-24
adding rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1'
  |=================================================================================================================================================================================| 100%

2023-09-15 13:09:03.582482 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/7db79cfb922_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
devel > packageVersion("spatialLIBD")
[1] ‘1.13.5’

Given that spatialLIBD 1.2.1 is from several years ago (Dec 17th, 2020 https://github.com/LieberInstitute/spatialLIBD/commit/a78c6d38a07baaa2d5e98e076ca49998ed67078c), can you check if it all works with a newer version?

Thanks! Leo