plotMarkerMap returns empty plot

[Michael-Geuenich]

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.

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