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samuel-marsh / scCustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
https://samuel-marsh.github.io/scCustomize/
GNU General Public License v3.0
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DimPlot_scCustom error:Error in .subset2(x, i, exact = exact) : subscript out of bounds #128

Closed Sophia409 closed 1 year ago

Sophia409 commented 1 year ago

Hi,

I can plot two metadata on umap by using funciton in Seurat, but couldn't plot it by using DimPlot_scCustom. Maybe you could help me figure out it here?

Would be greatly appreciated! Best regards and many thanks! Sophia

DimPlot(thalamus,pt.size = 1,label=T,label.size = 7,reduction = "umap",shuffle = T,raster = T,group.by = c('cell_type','development_stage') )
DimPlot_scCustom(Seuratob,pt.size = 1,label=T,label.size = 7,reduction = "umap",shuffle = T,raster = T,group.by = c('cell_type','development_stage'),num_columns = 2)
Error in .subset2(x, i, exact = exact) : subscript out of bounds
samuel-marsh commented 1 year ago

Hi Sophia,

Thanks for finding issue, I’ll see if I can figure out what issue is. In meantime could you please post the output of sessionInfo() here so I know what versions are potential issues.

Thanks! Sam

Sophia409 commented 1 year ago

Hi Sam,

This is my sessioninfo.

Thanks!

> sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8    LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                                LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] scCustomize_1.1.3    org.Mm.eg.db_3.17.0  hgu95av2.db_3.13.0   org.Mmu.eg.db_3.17.0 devtools_2.4.5       usethis_2.2.2        datapasta_3.1.0     
 [8] cowplot_1.1.1        ggplot2_3.4.3        org.Hs.eg.db_3.17.0  AnnotationDbi_1.62.2 IRanges_2.34.1       S4Vectors_0.38.1     Biobase_2.60.0      
[15] BiocGenerics_0.46.0  dplyr_1.1.3          patchwork_1.1.3      SeuratObject_4.1.3   Seurat_4.3.0.1      

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.21        splines_4.3.0           later_1.3.1             prismatic_1.1.1         bitops_1.0-7            tibble_3.2.1           
  [7] polyclip_1.10-4         janitor_2.2.0           lifecycle_1.0.3         globals_0.16.2          processx_3.8.2          lattice_0.21-8         
 [13] MASS_7.3-60             magrittr_2.0.3          plotly_4.10.2           remotes_2.4.2.1         httpuv_1.6.11           sctransform_0.4.0      
 [19] sp_2.0-0                sessioninfo_1.2.2       pkgbuild_1.4.2          spatstat.sparse_3.0-2   reticulate_1.32.0       pbapply_1.7-2          
 [25] DBI_1.1.3               RColorBrewer_1.1-3      lubridate_1.9.2         abind_1.4-5             pkgload_1.3.2.1         zlibbioc_1.46.0        
 [31] Rtsne_0.16              purrr_1.0.1             RCurl_1.98-1.12         circlize_0.4.15         GenomeInfoDbData_1.2.10 ggrepel_0.9.3          
 [37] irlba_2.3.5.1           listenv_0.9.0           spatstat.utils_3.0-3    goftest_1.2-3           spatstat.random_3.1-6   fitdistrplus_1.1-11    
 [43] parallelly_1.36.0       leiden_0.4.3            codetools_0.2-19        shape_1.4.6             tidyselect_1.2.0        farver_2.1.1           
 [49] matrixStats_1.0.0       spatstat.explore_3.2-3  jsonlite_1.8.4          ellipsis_0.3.2          progressr_0.14.0        ggridges_0.5.4         
 [55] survival_3.5-5          tools_4.3.0             ica_1.0-3               Rcpp_1.0.10             glue_1.6.2              gridExtra_2.3          
 [61] xfun_0.40               GenomeInfoDb_1.36.3     withr_2.5.0             BiocManager_1.30.20     fastmap_1.1.1           fansi_1.0.4            
 [67] callr_3.7.3             digest_0.6.31           timechange_0.2.0        R6_2.5.1                mime_0.12               ggprism_1.0.4          
 [73] colorspace_2.1-0        scattermore_1.2         tensor_1.5              spatstat.data_3.0-1     RSQLite_2.3.1           utf8_1.2.3             
 [79] tidyr_1.3.0             generics_0.1.3          data.table_1.14.8       prettyunits_1.1.1       httr_1.4.6              htmlwidgets_1.6.2      
 [85] uwot_0.1.16             pkgconfig_2.0.3         gtable_0.3.4            blob_1.2.4              lmtest_0.9-40           XVector_0.40.0         
 [91] htmltools_0.5.5         profvis_0.3.8           scales_1.2.1            png_0.1-8               snakecase_0.11.1        knitr_1.44             
 [97] rstudioapi_0.14         tzdb_0.4.0              reshape2_1.4.4          nlme_3.1-162            curl_5.0.0              GlobalOptions_0.1.2    
[103] cachem_1.0.8            zoo_1.8-12              stringr_1.5.0           KernSmooth_2.23-21      vipor_0.4.5             parallel_4.3.0         
[109] miniUI_0.1.1.1          ggrastr_1.0.2           pillar_1.9.0            grid_4.3.0              vctrs_0.6.2             RANN_2.6.1             
[115] urlchecker_1.0.1        promises_1.2.0.1        xtable_1.8-4            cluster_2.1.4           paletteer_1.5.0         beeswarm_0.4.0         
[121] evaluate_0.21           readr_2.1.4             cli_3.6.1               compiler_4.3.0          rlang_1.1.1             crayon_1.5.2           
[127] future.apply_1.11.0     labeling_0.4.3          rematch2_2.1.2          ps_1.7.5                forcats_1.0.0           ggbeeswarm_0.7.2       
[133] plyr_1.8.8              fs_1.6.3                stringi_1.7.12          viridisLite_0.4.2       deldir_1.0-9            munsell_0.5.0          
[139] Biostrings_2.68.1       lazyeval_0.2.2          spatstat.geom_3.2-5     Matrix_1.5-4.1          hms_1.1.3               bit64_4.0.5            
[145] future_1.33.0           KEGGREST_1.40.0         shiny_1.7.4             highr_0.10              ROCR_1.0-11             igraph_1.5.1           
[151] memoise_2.0.1           bit_4.0.5
samuel-marsh commented 1 year ago

Hi Sophia,

Found the issue which was due to a check I had for setting color palette. I have fixed the issue in the "develop_V5" branch (v1.9.9.9014). As SeuratV5 is backward compatible there should not be any issues updating onto this development branch. However, if you due notice issues with this or any other functions upon updating to "develop_V5" while still using Seurat V4 please let me know!

Best, Sam