Fail to obtain the spe data of DLPFC through fetch_data()
YSPeng1225 opened this issue · 6 comments
Hello,
Thanks for your supply of public Human DLPFC Visium dataset. However, when I follow the vignette you offer, I encountered the error as follow.
My code:
ehub <- ExperimentHub::ExperimentHub()
sce <- spatialLIBD::fetch_data(type = "spe", eh = ehub)
The error:
adding rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1'
Error in BiocFileCache::bfcrpath(bfc, url) :
not all 'rnames' found or unique.
In addition: Warning messages:
1: download failed
web resource path: ‘https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1’
local file path: ‘/Users/christine/Library/Caches/org.R-project.R/R/BiocFileCache/7b872905cae6_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1’
reason: Timeout was reached: [www.dropbox.com] Failed to connect to www.dropbox.com port 443 after 10005 ms: Timeout was reached
2: bfcadd() failed; resource removed
rid: BFC12
fpath: ‘https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1’
reason: download failed
3: In value[3L] :
trying to add rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1' produced error:
bfcadd() failed; see warnings()
The version info:
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Asia/Shanghai
tzcode source: internal
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] BiocFileCache_2.10.1 dbplyr_2.4.0 spatialLIBD_1.14.1
[4] SpatialExperiment_1.12.0 Seurat_5.0.2 SeuratObject_5.0.1
[7] sp_2.1-3 rugarch_1.5-1 rhdf5_2.46.1
[10] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 Biobase_2.62.0
[13] GenomicRanges_1.54.1 GenomeInfoDb_1.38.7 IRanges_2.36.0
[16] S4Vectors_0.40.2 BiocGenerics_0.48.1 MatrixGenerics_1.14.0
[19] matrixStats_1.2.0
loaded via a namespace (and not attached):
[1] spatstat.sparse_3.0-3 bitops_1.0-7
[3] httr_1.4.7 RColorBrewer_1.1-3
[5] doParallel_1.0.17 numDeriv_2016.8-1.1
[7] tools_4.3.1 sctransform_0.4.1
[9] utf8_1.2.4 R6_2.5.1
[11] DT_0.32 HDF5Array_1.30.1
[13] lazyeval_0.2.2 uwot_0.1.16
[15] rhdf5filters_1.14.1 withr_3.0.0
[17] prettyunits_1.2.0 gridExtra_2.3
[19] progressr_0.14.0 cli_3.6.2
[21] spatstat.explore_3.2-6 fastDummies_1.7.3
[23] fGarch_4032.91 sass_0.4.8
[25] mvtnorm_1.2-4 spatstat.data_3.0-4
[27] ggridges_0.5.6 pbapply_1.7-2
[29] Rsamtools_2.18.0 R.utils_2.12.3
[31] gbutils_0.5 scater_1.30.1
[33] sessioninfo_1.2.2 parallelly_1.37.1
[35] attempt_0.3.1 maps_3.4.2
[37] limma_3.58.1 rstudioapi_0.15.0
[39] RSQLite_2.3.5 BiocIO_1.12.0
[41] generics_0.1.3 ica_1.0-3
[43] spatstat.random_3.2-3 dplyr_1.1.4
[45] Matrix_1.6-5 ggbeeswarm_0.7.2
[47] DANA_1.3.0 fansi_1.0.6
[49] abind_1.4-5 R.methodsS3_1.8.2
[51] lifecycle_1.0.4 yaml_2.3.8
[53] edgeR_4.0.16 SparseArray_1.2.4
[55] Rtsne_0.17 paletteer_1.6.0
[57] grid_4.3.1 blob_1.2.4
[59] dqrng_0.3.2 promises_1.2.1
[61] ExperimentHub_2.10.0 crayon_1.5.2
[63] miniUI_0.1.1.1 lattice_0.22-5
[65] beachmat_2.18.1 cowplot_1.1.3
[67] KEGGREST_1.42.0 magick_2.8.3
[69] pillar_1.9.0 rjson_0.2.21
[71] future.apply_1.11.1 codetools_0.2-19
[73] leiden_0.4.3.1 glue_1.7.0
[75] data.table_1.15.2 vctrs_0.6.5
[77] png_0.1-8 spam_2.10-0
[79] Rdpack_2.6 gtable_0.3.4
[81] rematch2_2.1.2 cachem_1.0.8
[83] ks_1.14.2 DropletUtils_1.22.0
[85] rbibutils_2.2.16 S4Arrays_1.2.1
[87] mime_0.12 GeneralizedHyperbolic_0.8-6
[89] pracma_2.4.4 survival_3.5-8
[91] timeDate_4032.109 iterators_1.0.14
[93] fields_15.2 statmod_1.5.0
[95] interactiveDisplayBase_1.40.0 ellipsis_0.3.2
[97] fitdistrplus_1.1-11 ROCR_1.0-11
[99] nlme_3.1-164 spd_2.0-1
[101] xts_0.13.2 bit64_4.0.5
[103] filelock_1.0.3 RcppAnnoy_0.0.22
[105] cvar_0.5 fBasics_4032.96
[107] bslib_0.6.1 irlba_2.3.5.1
[109] vipor_0.4.7 KernSmooth_2.23-22
[111] colorspace_2.1-0 DBI_1.2.2
[113] tidyselect_1.2.0 timeSeries_4032.109
[115] bit_4.0.5 compiler_4.3.1
[117] curl_5.2.1 BiocNeighbors_1.20.2
[119] DelayedArray_0.28.0 plotly_4.10.4
[121] rtracklayer_1.62.0 scales_1.3.0
[123] lmtest_0.9-40 spatial_7.3-17
[125] rappdirs_0.3.3 stringr_1.5.1
[127] digest_0.6.34 goftest_1.2-3
[129] spatstat.utils_3.0-4 benchmarkmeData_1.0.4
[131] XVector_0.42.0 htmltools_0.5.7
[133] pkgconfig_2.0.3 sparseMatrixStats_1.14.0
[135] fastmap_1.1.1 rlang_1.1.3
[137] htmlwidgets_1.6.4 DelayedMatrixStats_1.24.0
[139] shiny_1.8.0 jquerylib_0.1.4
[141] zoo_1.8-12 jsonlite_1.8.8
[143] BiocParallel_1.36.0 mclust_6.1
[145] R.oo_1.26.0 config_0.3.2
[147] BiocSingular_1.18.0 RCurl_1.98-1.14
[149] magrittr_2.0.3 scuttle_1.12.0
[151] GenomeInfoDbData_1.2.11 dotCall64_1.1-1
[153] patchwork_1.2.0 Rhdf5lib_1.24.2
[155] munsell_0.5.0 Rcpp_1.0.12
[157] viridis_0.6.5 reticulate_1.35.0
[159] lobstr_1.1.2 stringi_1.8.3
[161] zlibbioc_1.48.0 MASS_7.3-60.0.1
[163] AnnotationHub_3.10.0 plyr_1.8.9
[165] listenv_0.9.1 ggrepel_0.9.5
[167] deldir_2.0-4 SkewHyperbolic_0.4-2
[169] Biostrings_2.70.2 splines_4.3.1
[171] tensor_1.5 locfit_1.5-9.9
[173] igraph_2.0.2 spatstat.geom_3.2-9
[175] RcppHNSW_0.6.0 ScaledMatrix_1.10.0
[177] reshape2_1.4.4 XML_3.99-0.16.1
[179] BiocVersion_3.18.1 golem_0.4.1
[181] DistributionUtils_0.6-1 BiocManager_1.30.22
[183] nloptr_2.0.3 foreach_1.5.2
[185] httpuv_1.6.14 RANN_2.6.1
[187] tidyr_1.3.1 purrr_1.0.2
[189] polyclip_1.10-6 future_1.33.1
[191] benchmarkme_1.0.8 scattermore_1.2
[193] ggplot2_3.5.0 rsvd_1.0.5
[195] xtable_1.8-4 restfulr_0.0.15
[197] RSpectra_0.16-1 Rsolnp_1.16
[199] later_1.3.2 viridisLite_0.4.2
[201] truncnorm_1.0-9 tibble_3.2.1
[203] beeswarm_0.4.0 GenomicAlignments_1.38.2
[205] memoise_2.0.1 AnnotationDbi_1.64.1
[207] cluster_2.1.6 shinyWidgets_0.8.2
[209] globals_0.16.3
I have found that this may be a casual issue due to the internet, yet I failed to find the dataset download link from previous issues.
I'll appreciate it if you could provide the spatial data with manual annotations at your convenience.
Hi,
What happens if you click on https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1 on your browser?
From what you report, it seems that for some reason Dropbox access is blocked at your current location. Try using a different network (WiFi typically) from a different ISP.
Best,
Leo
Hi,
What happens if you click on https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1 on your browser?
From what you report, it seems that for some reason Dropbox access is blocked at your current location. Try using a different network (WiFi typically) from a different ISP.
Best, Leo
Thanks for your in-time reply! The link you offer seemingly refers to the single cell expression dataset. What I need is spatial dataset containing the slot coordinates the manual annotations(always known as ground truth).
Hi,
From https://research.libd.org/spatialLIBD/reference/fetch_data.html, it seems like you want to run:
library("spatialLIBD")
spe <- fetch_data("spe")That will download the data from https://doi.org/10.1038/s41593-020-00787-0.
If it errors out, you'll see the Dropbox link to the file you wanted to download.
Internally, using fetch_data("spe") uses
Lines 119 to 122 in 079a0f8
fetch_data("sce") (aka Lines 125 to 143 in 079a0f8
sce_to_spe(). See https://research.libd.org/spatialLIBD/reference/sce_to_spe.html.
Best,
Leo
Thanks! I have downloaded the single cell expression dataset from your https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1. But I failed again when I tried to transform the sce into spe and the error is as `load('/Users/christine/Downloads/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata')
spe <- sce_to_spe(sce, imageData = NULL)
Error in check_sce(sce) :
all(c("imagerow", "imagecol", "sample_name", "key", variables) %in% .... is not TRUE`
Hi,
From https://research.libd.org/spatialLIBD/reference/fetch_data.html, it seems like you want to run:
library("spatialLIBD") spe <- fetch_data("spe")That will download the data from https://doi.org/10.1038/s41593-020-00787-0.
If it errors out, you'll see the Dropbox link to the file you wanted to download.
Internally, using
fetch_data("spe")usesLines 119 to 122 in 079a0f8
which first calls
fetch_data("sce")(aka
Lines 125 to 143 in 079a0f8
and related code; this includes the actual Dropbox link to the file you are trying to download), then runs
sce_to_spe(). See https://research.libd.org/spatialLIBD/reference/sce_to_spe.html.
Best, Leo
You really need to provide reprex::reprex() output along with the sessioninfo::session_info() to make it easier to follow what you are doing + identify the root issue. Seems like you missed an internal step in spatialLIBD::fetch_data() which is the spatialLIBD:::.update_sce() call from
Line 276 in 079a0f8
Here's a full working reprex:
## Download the file from Dropbox (you are doing this with your browser)
local_file <-
tempfile("Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata")
download.file(
"https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1",
local_file,
mode = "wb"
)
tools::md5sum(local_file)
#> /var/folders/_2/hqcmhc1d1bl3lqxgcrkpv8_00000gn/T//RtmpsIXvrT/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata1580d117c1ca8
#> "bc17fa34db140ce73c563c58eb074432"
## Since it seems like the Dropbox download is not working for you
## via BiocFileCache::bfcrpath() [the function used internally by
## spatialLIBD::fetch_data() ], you are downloading the file
## manually. Make sure that the md5sum matches the info shown above.
## Load the data
suppressPackageStartupMessages(library("spatialLIBD"))
load(local_file, verbose = TRUE)
#> Loading objects:
#> sce
## Do the steps that are done internally by spatialLIBD::fetch_data()
## to update the original SingleCellExperiment object (SCE) into
## a valid SpatialExperimentObject
spe <- spatialLIBD::sce_to_spe(spatialLIBD:::.update_sce(sce))
## It works
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
## Plot the logcounts for the MBP gene
vis_gene(spe,
geneid = rowData(spe)$gene_search[rowData(spe)$gene_name == "MBP"],
point_size = 1
)
## Plot the manually annotated layers (clusters)
vis_clus(spe, clustervar = "spatialLIBD", point_size = 1)
## R reproducibility information
options(width = 120)
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.3.2 (2023-10-31)
#> os macOS Sonoma 14.3.1
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2024-03-23
#> pandoc 3.1.12.1 @ /opt/homebrew/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
#> AnnotationDbi 1.64.1 2023-11-02 [1] Bioconductor
#> AnnotationHub 3.10.0 2023-10-26 [1] Bioconductor
#> attempt 0.3.1 2020-05-03 [1] CRAN (R 4.3.0)
#> beachmat 2.18.1 2024-02-17 [1] Bioconductor 3.18 (R 4.3.2)
#> beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.3.0)
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#> BiocIO 1.12.0 2023-10-26 [1] Bioconductor
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#> BiocParallel 1.36.0 2023-10-26 [1] Bioconductor
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#> bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
#> blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
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#> cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
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#> config 0.3.2 2023-08-30 [1] CRAN (R 4.3.0)
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#>
#> [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────Created on 2024-03-23 with reprex v2.1.0
I'm closing this issue for inactivity.