[BUG] fetch_data(type = "spe") yields "Error: Other 'type' values are not supported."
george-hall-ucl opened this issue · comments
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.
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()isTRUE-- NO
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 a78c6d3), can you check if it all works with a newer version?
Thanks!
Leo