Open Michael-Geuenich opened 4 months ago
Hi, thank you for creating this package.
I've tried running it using the example data provided in the vignette, but am running into issues with the plotMarkerMap function as it only returns an empty plot as shown below.
plotMarkerMap
This is the code I ran
library(SoupX) tmpDir = tempdir(check = TRUE) download.file("https://cf.10xgenomics.com/samples/cell-exp/2.1.0/pbmc4k/pbmc4k_raw_gene_bc_matrices.tar.gz", destfile = file.path(tmpDir, "tod.tar.gz")) download.file("https://cf.10xgenomics.com/samples/cell-exp/2.1.0/pbmc4k/pbmc4k_filtered_gene_bc_matrices.tar.gz", destfile = file.path(tmpDir, "toc.tar.gz")) untar(file.path(tmpDir, "tod.tar.gz"), exdir = tmpDir) untar(file.path(tmpDir, "toc.tar.gz"), exdir = tmpDir) toc = Seurat::Read10X(file.path(tmpDir, "filtered_gene_bc_matrices", "GRCh38")) tod = Seurat::Read10X(file.path(tmpDir, "raw_gene_bc_matrices", "GRCh38")) sc = SoupChannel(tod, toc) data(PBMC_metaData) sc = setClusters(sc, setNames(PBMC_metaData$Cluster, rownames(PBMC_metaData))) sc = setDR(sc, PBMC_metaData[colnames(sc$toc), c("RD1", "RD2")]) library(ggplot2) cells <- colnames(as.matrix(sc$toc)) # this was required to fix the problem mentioned in issue 98 (https://github.com/constantAmateur/SoupX/issues/98) cells <- gsub("-1", "", cells) dd = PBMC_metaData[cells, ] dd$IGKC = sc$toc["IGKC", ] plotMarkerMap(sc, "IGKC")
My session info
R version 4.3.2 (2023-10-31) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.0.1 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-x86_64/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: America/Toronto tzcode source: internal attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] SoupX_1.6.2 scran_1.30.2 patchwork_1.2.0 ggpubr_0.6.0 [5] scater_1.30.1 scuttle_1.12.0 ggrepel_0.9.5 ComplexHeatmap_2.18.0 [9] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 [13] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 [17] ggplot2_3.5.1 tidyverse_2.0.0 SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 [21] Biobase_2.62.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 IRanges_2.36.0 [25] S4Vectors_0.40.2 BiocGenerics_0.48.1 MatrixGenerics_1.14.0 matrixStats_1.3.0 loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.3.2 later_1.3.2 bitops_1.0-7 [5] R.oo_1.26.0 polyclip_1.10-6 fastDummies_1.7.3 lifecycle_1.0.4 [9] rstatix_0.7.2 edgeR_4.0.16 doParallel_1.0.17 vroom_1.6.5 [13] globals_0.16.3 lattice_0.22-6 MASS_7.3-60.0.1 backports_1.4.1 [17] magrittr_2.0.3 limma_3.58.1 plotly_4.10.4 metapod_1.10.1 [21] httpuv_1.6.15 Seurat_5.0.3 sctransform_0.4.1 spam_2.10-0 [25] sp_2.1-4 spatstat.sparse_3.0-3 reticulate_1.37.0 cowplot_1.1.3 [29] pbapply_1.7-2 RColorBrewer_1.1-3 pkgload_1.3.4 abind_1.4-5 [33] zlibbioc_1.48.2 Rtsne_0.17 R.utils_2.12.3 RCurl_1.98-1.14 [37] circlize_0.4.16 GenomeInfoDbData_1.2.11 irlba_2.3.5.1 listenv_0.9.1 [41] spatstat.utils_3.0-4 goftest_1.2-3 RSpectra_0.16-1 dqrng_0.4.0 [45] spatstat.random_3.2-3 fitdistrplus_1.1-11 parallelly_1.37.1 DelayedMatrixStats_1.24.0 [49] leiden_0.4.3.1 codetools_0.2-20 DelayedArray_0.28.0 tidyselect_1.2.1 [53] shape_1.4.6.1 farver_2.1.2 viridis_0.6.5 ScaledMatrix_1.10.0 [57] spatstat.explore_3.2-7 jsonlite_1.8.8 GetoptLong_1.0.5 BiocNeighbors_1.20.2 [61] progressr_0.14.0 ggridges_0.5.6 survival_3.6-4 iterators_1.0.14 [65] foreach_1.5.2 tools_4.3.2 ica_1.0-3 Rcpp_1.0.12 [69] glue_1.7.0 gridExtra_2.3 SparseArray_1.2.4 mgcv_1.9-1 [73] withr_3.0.0 fastmap_1.2.0 bluster_1.12.0 fansi_1.0.6 [77] digest_0.6.35 rsvd_1.0.5 timechange_0.3.0 R6_2.5.1 [81] mime_0.12 colorspace_2.1-0 Cairo_1.6-2 scattermore_1.2 [85] tensor_1.5 spatstat.data_3.0-4 R.methodsS3_1.8.2 utf8_1.2.4 [89] generics_0.1.3 data.table_1.15.4 httr_1.4.7 htmlwidgets_1.6.4 [93] S4Arrays_1.2.1 uwot_0.2.2 pkgconfig_2.0.3 gtable_0.3.5 [97] rsconnect_1.2.2 lmtest_0.9-40 XVector_0.42.0 htmltools_0.5.8.1 [101] carData_3.0-5 dotCall64_1.1-1 clue_0.3-65 SeuratObject_5.0.2 [105] scales_1.3.0 png_0.1-8 rstudioapi_0.16.0 tzdb_0.4.0 [109] reshape2_1.4.4 rjson_0.2.21 nlme_3.1-164 zoo_1.8-12 [113] GlobalOptions_0.1.2 KernSmooth_2.23-24 vipor_0.4.7 parallel_4.3.2 [117] miniUI_0.1.1.1 pillar_1.9.0 vctrs_0.6.5 RANN_2.6.1 [121] promises_1.3.0 car_3.1-2 BiocSingular_1.18.0 beachmat_2.18.1 [125] xtable_1.8-4 cluster_2.1.6 beeswarm_0.4.0 magick_2.8.3 [129] locfit_1.5-9.9 cli_3.6.2 compiler_4.3.2 rlang_1.1.3 [133] crayon_1.5.2 ggsignif_0.6.4 future.apply_1.11.2 labeling_0.4.3 [137] ggbeeswarm_0.7.2 plyr_1.8.9 stringi_1.8.4 viridisLite_0.4.2 [141] deldir_2.0-4 BiocParallel_1.36.0 munsell_0.5.1 lazyeval_0.2.2 [145] spatstat.geom_3.2-9 Matrix_1.6-5 RcppHNSW_0.6.0 hms_1.1.3 [149] bit64_4.0.5 sparseMatrixStats_1.14.0 future_1.33.2 statmod_1.5.0 [153] shiny_1.8.1.1 ROCR_1.0-11 broom_1.0.6 igraph_2.0.3 [157] bit_4.0.5
Hi, thank you for creating this package.
I've tried running it using the example data provided in the vignette, but am running into issues with the
plotMarkerMapfunction as it only returns an empty plot as shown below.This is the code I ran
My session info