setting combine = FALSE in FeaturePlot_scCustomize() returns NULL

[nikofleischer]

There seems to be a problem when the combine = FALSE flag is set in FeaturePlot_scCustomize(). The function call simply returns NULL. Find mwe below, thanks a lot for your help!
Best, Niko

library(Seurat)
library(SeuratData)
library(scCustomize)
library(dplyr)
InstallData("pbmc3k")
data("pbmc3k")
pbmc = pbmc3k %>% 
  NormalizeData() %>% 
  ScaleData() %>% 
  FindVariableFeatures() %>%  
  RunPCA() %>% 
  RunUMAP(dims = 1:10)
FeaturePlot(pbmc,features = c('NRG1','ERBB2'), combine = FALSE)
FeaturePlot_scCustom(pbmc,features = c('NRG1','ERBB2'), combine = FALSE)

Output:

>  x 

[[1]]
[[2]]

> y

NULL

SessionInfo:

R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] pbmc3k.SeuratData_3.1.4 scCustomize_0.7.0       SeuratData_0.2.1        SeuratObject_4.0.4      Seurat_4.1.0           
[6] dplyr_1.0.8            

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  reticulate_1.24             tidyselect_1.1.2            htmlwidgets_1.5.4          
  [5] grid_4.1.2                  Rtsne_0.15                  devtools_2.4.3              munsell_0.5.0              
  [9] codetools_0.2-18            ica_1.0-2                   future_1.24.0               miniUI_0.1.1.1             
 [13] withr_2.5.0                 spatstat.random_2.2-0       colorspace_2.0-3            Biobase_2.54.0             
 [17] rstudioapi_0.13             stats4_4.1.2                SingleCellExperiment_1.16.0 ROCR_1.0-11                
 [21] ggsignif_0.6.3              tensor_1.5                  listenv_0.8.0               labeling_0.4.2             
 [25] MatrixGenerics_1.6.0        GenomeInfoDbData_1.2.7      polyclip_1.10-0             farver_2.1.0               
 [29] pheatmap_1.0.12             rprojroot_2.0.3             parallelly_1.30.0           vctrs_0.4.0                
 [33] generics_0.1.2              dittoSeq_1.7.0              R6_2.5.1                    GenomeInfoDb_1.30.1        
 [37] ggbeeswarm_0.6.0            bitops_1.0-7                spatstat.utils_2.3-0        cachem_1.0.6               
 [41] DelayedArray_0.20.0         promises_1.2.0.1            scales_1.1.1                beeswarm_0.4.0             
 [45] gtable_0.3.0                globals_0.14.0              processx_3.5.3              goftest_1.2-3              
 [49] rlang_1.0.2                 GlobalOptions_0.1.2         splines_4.1.2               rstatix_0.7.0              
 [53] lazyeval_0.2.2              spatstat.geom_2.4-0         broom_0.7.12                reshape2_1.4.4             
 [57] abind_1.4-5                 backports_1.4.1             httpuv_1.6.5                tools_4.1.2                
 [61] usethis_2.1.5               ggplot2_3.3.5               ellipsis_0.3.2              spatstat.core_2.4-2        
 [65] RColorBrewer_1.1-3          BiocGenerics_0.40.0         sessioninfo_1.2.2           ggridges_0.5.3             
 [69] Rcpp_1.0.8.3                plyr_1.8.7                  zlibbioc_1.40.0             purrr_0.3.4                
 [73] RCurl_1.98-1.6              ps_1.6.0                    prettyunits_1.1.1           ggpubr_0.4.0               
 [77] rpart_4.1.16                deldir_1.0-6                pbapply_1.5-0               viridis_0.6.2              
 [81] cowplot_1.1.1               S4Vectors_0.32.4            zoo_1.8-9                   SummarizedExperiment_1.24.0
 [85] ggrepel_0.9.1               cluster_2.1.2               fs_1.5.2                    magrittr_2.0.3             
 [89] RSpectra_0.16-0             data.table_1.14.2           scattermore_0.8             circlize_0.4.14            
 [93] lmtest_0.9-40               RANN_2.6.1                  fitdistrplus_1.1-8          matrixStats_0.61.0         
 [97] pkgload_1.2.4               patchwork_1.1.1             mime_0.12                   xtable_1.8-4               
[101] IRanges_2.28.0              gridExtra_2.3               shape_1.4.6                 testthat_3.1.3             
[105] compiler_4.1.2              tibble_3.1.6                colorway_0.2.0              KernSmooth_2.23-20         
[109] crayon_1.5.1                htmltools_0.5.2             mgcv_1.8-39                 later_1.3.0                
[113] ggprism_1.0.3.9000          tidyr_1.2.0                 lubridate_1.8.0             MASS_7.3-55                
[117] rappdirs_0.3.3              Matrix_1.4-0                car_3.0-12                  brio_1.1.3                 
[121] cli_3.2.0                   parallel_4.1.2              igraph_1.3.0                GenomicRanges_1.46.1       
[125] forcats_0.5.1               pkgconfig_2.0.3             plotly_4.10.0               spatstat.sparse_2.1-0      
[129] paletteer_1.4.0             vipor_0.4.5                 XVector_0.34.0              snakecase_0.11.0           
[133] stringr_1.4.0               callr_3.7.0                 digest_0.6.29               sctransform_0.3.3          
[137] RcppAnnoy_0.0.19            janitor_2.1.0               spatstat.data_2.1-4         leiden_0.3.9               
[141] uwot_0.1.11                 curl_4.3.2                  shiny_1.7.1                 lifecycle_1.0.1            
[145] nlme_3.1-155                jsonlite_1.8.0              carData_3.0-5               desc_1.4.1                 
[149] viridisLite_0.4.0           fansi_1.0.3                 pillar_1.7.0                lattice_0.20-45            
[153] fastmap_1.1.0               httr_1.4.2                  pkgbuild_1.3.1              survival_3.3-1             
[157] glue_1.6.2                  remotes_2.4.2               png_0.1-7                   stringi_1.7.6              
[161] rematch2_2.1.2              memoise_2.0.1               renv_0.15.4                 irlba_2.3.5                
[165] future.apply_1.8.1         

[samuel-marsh]

Hi Niko,

Interesting, I’ll take look into it. Thanks for providing example!

Best,
Sam

[samuel-marsh]

Hi Niko,

Ok should be all set now in dev branch (v0.7.0.0028). I'm going to close this now but if fix doesn't work for you please let me know and I'll reopen issue.

Thanks again!
Sam

[Brawni]

Hello @samuel-marsh!
Great package! I'm having the same issue here. Running on package version 2.0.1.9006.
Thanks!

[samuel-marsh]

@Brawni do you mind submitting new issue with code you are running and output of sessionInfo?

Thanks!
Sam

[XiaolongYang-HZAU]

[1] ‘2.1.2’ version seems have the same problem ，when i set conbian to FALSE，i get error like:Error in withCallingHandlers(expr, message = function(c) if (inherits(c, "missingObject")): Object 'p' not found.

[samuel-marsh]

@XiaolongYang-HZAU,

I have just fixed this and working again in develop branch v2.1.2.9035. If you continue to have any issues with combine please open new issue and I'll be happy to help more!

Best,
Sam