Closed YSPeng1225 closed 4 months ago
lcolladotor
commented
5 months ago 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
YSPeng1225
commented
5 months ago 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).
lcolladotor
commented
5 months ago 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 https://github.com/LieberInstitute/spatialLIBD/blob/079a0f84e0f1026f84c085dfbf614a589914a653/R/fetch_data.R#L119-L122 which first calls fetch_data("sce") (aka https://github.com/LieberInstitute/spatialLIBD/blob/079a0f84e0f1026f84c085dfbf614a589914a653/R/fetch_data.R#L125-L143 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
YSPeng1225
commented
5 months ago 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")useswhich first calls
fetch_data("sce")(aka https://github.com/LieberInstitute/spatialLIBD/blob/079a0f84e0f1026f84c085dfbf614a589914a653/R/fetch_data.R#L125-L143and 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
lcolladotor
commented
5 months ago 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 https://github.com/LieberInstitute/spatialLIBD/blob/079a0f84e0f1026f84c085dfbf614a589914a653/R/fetch_data.R#L276.
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
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#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2024-03-23
#> pandoc 3.1.12.1 @ /opt/homebrew/bin/ (via rmarkdown)
#>
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lcolladotor
commented
4 months ago I'm closing this issue for inactivity.
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.