Plots not printing

[hcjarnagin]

All scCustomize/Nebulosa Plots are not printing to my R version. If I use ggplot2 versions > 3.4.4 I receive this error:

Error in Plot_Density_Custom(): ! Due to error in Nebulosa package and ggplot2 v3.5.0 Plot_Density_Custom functionality is currently restricted to ggplot v3.4.4 or lower.

If I use ggplot2 versions <= 3.4.4, the plots simply print to a blank screen. I can save them as an object and see the elements in the object lists, but can't print to a PDF, Tiff, or even make it visible.

Do you have any suggestions?

# insert reproducible example here

DefaultAssay(test)<-"SCT"

scCustomize::Plot_Density_Custom(test, reduction = "rna_fib_umap", features=c("PDGFB", "PDGFA", "PDGFRB", "PDGFRA"))

PASTE HERE sessionInfo() output

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

other attached packages:
 [1] scGSVA_0.0.21          org.Hs.eg.db_3.19.1    AnnotationDbi_1.66.0   IRanges_2.38.0        
 [5] S4Vectors_0.42.0       KEGGREST_1.44.0        gprofiler2_0.2.3       Libra_1.7             
 [9] nnls_1.5               EnhancedVolcano_1.22.0 ggrepel_0.9.5          Nebulosa_1.0.1        
[13] patchwork_1.2.0        scCustomize_2.1.2.9041 ComplexHeatmap_2.20.0  msigdbr_7.5.1         
[17] biomaRt_2.60.0         harmony_1.2.0          speckle_0.0.3          lubridate_1.9.3       
[21] forcats_1.0.0          stringr_1.5.1          purrr_1.0.2            readr_2.1.5           
[25] tidyr_1.3.1            tibble_3.2.1           tidyverse_2.0.0        presto_1.0.0          
[29] data.table_1.15.4      Rcpp_1.0.12            Signac_1.12.0          SeuratObject_5.0.1    
[33] Seurat_4.4.0           CellChat_2.1.2         Biobase_2.64.0         BiocGenerics_0.50.0   
[37] ggplot2_3.5.1          igraph_2.0.3           dplyr_1.1.4           

loaded via a namespace (and not attached):
  [1] GSEABase_1.64.0             progress_1.2.3              urlchecker_1.0.1           
  [4] goftest_1.2-3               HDF5Array_1.30.1            Biostrings_2.72.0          
  [7] vctrs_0.6.5                 spatstat.random_3.2-3       digest_0.6.35              
 [10] png_0.1-8                   shape_1.4.6.1               registry_0.5-1             
 [13] org.Mm.eg.db_3.19.1         deldir_2.0-4                parallelly_1.37.1          
 [16] MASS_7.3-60.2               reshape2_1.4.4              httpuv_1.6.15              
 [19] foreach_1.5.2               withr_3.0.0                 ggrastr_1.0.2              
 [22] xfun_0.43                   ggpubr_0.6.0                ellipsis_0.3.2             
 [25] survival_3.5-8              memoise_2.0.1               ggbeeswarm_0.7.2           
 [28] janitor_2.2.0               profvis_0.3.8               systemfonts_1.0.6          
 [31] zoo_1.8-12                  GlobalOptions_0.1.2         pbapply_1.7-2              
 [34] prettyunits_1.2.0           rematch2_2.1.2              promises_1.3.0             
 [37] httr_1.4.7                  rstatix_0.7.2               rhdf5filters_1.16.0        
 [40] globals_0.16.3              fitdistrplus_1.1-11         rhdf5_2.48.0               
 [43] ps_1.7.6                    rstudioapi_0.16.0           UCSC.utils_1.0.0           
 [46] miniUI_0.1.1.1              generics_0.1.3              processx_3.8.4             
 [49] ggalluvial_0.12.5           babelgene_22.9              curl_5.2.1                 
 [52] zlibbioc_1.50.0             ScaledMatrix_1.12.0         polyclip_1.10-6            
 [55] GenomeInfoDbData_1.2.12     SparseArray_1.4.3           desc_1.4.3                 
 [58] xtable_1.8-4                pracma_2.4.4                doParallel_1.0.17          
 [61] evaluate_0.23               S4Arrays_1.4.0              BiocFileCache_2.12.0       
 [64] hms_1.1.3                   GenomicRanges_1.56.0        irlba_2.3.5.1              
 [67] colorspace_2.1-0            filelock_1.0.3              ggnetwork_0.5.13           
 [70] ROCR_1.0-11                 reticulate_1.36.1           spatstat.data_3.0-4        
 [73] snakecase_0.11.1            magrittr_2.0.3              lmtest_0.9-40              
 [76] viridis_0.6.5               later_1.3.2                 lattice_0.22-6             
 [79] spatstat.geom_3.2-9         NMF_0.27                    future.apply_1.11.2        
 [82] XML_3.99-0.16.1             scattermore_1.2             scuttle_1.14.0             
 [85] cowplot_1.1.3               matrixStats_1.3.0           RcppAnnoy_0.0.22           
 [88] pillar_1.9.0                nlme_3.1-164                iterators_1.0.14           
 [91] sna_2.7-2                   gridBase_0.4-7              compiler_4.4.0             
 [94] beachmat_2.20.0             RSpectra_0.16-1             stringi_1.8.4              
 [97] tensor_1.5                  SummarizedExperiment_1.34.0 devtools_2.4.5             
[100] plyr_1.8.9                  crayon_1.5.2                abind_1.4-5                
[103] locfit_1.5-9.9              sp_2.1-4                    bit_4.0.5                  
[106] fastmatch_1.1-4             codetools_0.2-20            BiocSingular_1.20.0        
[109] bslib_0.7.0                 paletteer_1.6.0             GetoptLong_1.0.5           
[112] plotly_4.10.4               mime_0.12                   splines_4.4.0              
[115] circlize_0.4.16             dbplyr_2.5.0                sparseMatrixStats_1.16.0   
[118] knitr_1.46                  blob_1.2.4                  utf8_1.2.4                 
[121] clue_0.3-65                 fs_1.6.4                    listenv_0.9.1              
[124] DelayedMatrixStats_1.26.0   GSVA_1.50.5                 pkgbuild_1.4.4             
[127] ggsignif_0.6.4              Matrix_1.7-0                callr_3.7.6                
[130] statmod_1.5.0               tzdb_0.4.0                  svglite_2.1.3              
[133] pheatmap_1.0.12             pkgconfig_2.0.3             network_1.18.2             
[136] tools_4.4.0                 cachem_1.0.8                RSQLite_2.3.6              
[139] viridisLite_0.4.2           DBI_1.2.2                   fastmap_1.1.1              
[142] rmarkdown_2.26              scales_1.3.0                usethis_2.2.3              
[145] ica_1.0-3                   Rsamtools_2.20.0            broom_1.0.5                
[148] sass_0.4.9                  coda_0.19-4.1               FNN_1.1.4                  
[151] ggprism_1.0.5               BiocManager_1.30.23         dotCall64_1.1-1            
[154] graph_1.80.0                carData_3.0-5               RANN_2.6.1                 
[157] farver_2.1.1                yaml_2.3.8                  MatrixGenerics_1.16.0      
[160] cli_3.6.2                   leiden_0.4.3.1              lifecycle_1.0.4            
[163] uwot_0.2.2                  mvtnorm_1.2-4               sessioninfo_1.2.2          
[166] backports_1.4.1             annotate_1.82.0             BiocParallel_1.38.0        
[169] timechange_0.3.0            gtable_0.3.5                rjson_0.2.21               
[172] ggridges_0.5.6              progressr_0.14.0            parallel_4.4.0             
[175] limma_3.60.0                jsonlite_1.8.8              edgeR_4.2.0                
[178] bitops_1.0-7                bit64_4.0.5                 Rtsne_0.17                 
[181] spatstat.utils_3.0-4        BiocNeighbors_1.22.0        jquerylib_0.1.4            
[184] lazyeval_0.2.2              shiny_1.8.1.1               htmltools_0.5.8.1          
[187] sctransform_0.4.1           rappdirs_0.3.3              glue_1.7.0                 
[190] spam_2.10-0                 httr2_1.0.1                 XVector_0.44.0             
[193] mclust_6.1.1                ks_1.14.2                   gridExtra_2.3              
[196] R6_2.5.1                    SingleCellExperiment_1.26.0 labeling_0.4.3             
[199] RcppRoll_0.3.0              cluster_2.1.6               rngtools_1.5.2             
[202] Rhdf5lib_1.24.2             pkgload_1.3.4               GenomeInfoDb_1.40.0        
[205] statnet.common_4.9.0        DelayedArray_0.30.1         tidyselect_1.2.1           
[208] vipor_0.4.7                 xml2_1.3.6                  car_3.1-2                  
[211] future_1.33.2               rsvd_1.0.5                  munsell_0.5.1              
[214] KernSmooth_2.23-22          htmlwidgets_1.6.4           RColorBrewer_1.1-3         
[217] rlang_1.1.3                 spatstat.sparse_3.0-3       spatstat.explore_3.2-7     
[220] remotes_2.5.0               fansi_1.0.6                 beeswarm_0.4.0      

[samuel-marsh]

Hi @hcjarnagin,

I think the issue is likely with your version of Nebulosa. Can you update to latest dev branch of scCustomize ("release/2.0.0") and then run BiocManager::install("Nebulosa") to update Nebulosa and see if that fixes issue. If not can you provide reproducible example with pbmc data from SeuratData package? I'm unable to replicate issue on my end.

Best, Sam

library(tidyverse)
library(Seurat)
#> Loading required package: SeuratObject
#> Loading required package: sp
#> 
#> Attaching package: 'SeuratObject'
#> The following objects are masked from 'package:base':
#> 
#>     intersect, t
library(scCustomize)
#> scCustomize v2.1.2.9063
#> If you find the scCustomize useful please cite.
#> See 'samuel-marsh.github.io/scCustomize/articles/FAQ.html' for citation info.

pbmc <- pbmc3k.SeuratData::pbmc3k.final
pbmc <- suppressMessages(UpdateSeuratObject(pbmc))
#> Warning: Assay RNA changing from Assay to Assay
#> Warning: Graph RNA_nn changing from Graph to Graph
#> Warning: Graph RNA_snn changing from Graph to Graph
#> Warning: DimReduc pca changing from DimReduc to DimReduc
#> Warning: DimReduc umap changing from DimReduc to DimReduc
#> Warning: Adding a command log without an assay associated with it
#> Adding a command log without an assay associated with it

Plot_Density_Custom(pbmc, "CD14")

^{Created on 2024-05-14 with reprex v2.1.0}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.4.0 (2024-04-24) #> os macOS Monterey 12.7.4 #> system x86_64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz America/New_York #> date 2024-05-14 #> pandoc 3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/x86_64/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> abind 1.4-5 2016-07-21 [1] CRAN (R 4.4.0) #> beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.4.0) #> Biobase 2.64.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) #> BiocGenerics 0.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) #> Cairo 1.6-2 2023-11-28 [1] CRAN (R 4.4.0) #> circlize 0.4.16 2024-02-20 [1] CRAN (R 4.4.0) #> cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.0) #> cluster 2.1.6 2023-12-01 [1] CRAN (R 4.4.0) #> codetools 0.2-20 2024-03-31 [1] CRAN (R 4.4.0) #> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.4.0) #> cowplot 1.1.3 2024-01-22 [1] CRAN (R 4.4.0) #> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.4.0) #> curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.0) #> data.table 1.15.4 2024-03-30 [1] CRAN (R 4.4.0) #> DelayedArray 0.30.1 2024-05-07 [1] Bioconductor 3.19 (R 4.4.0) #> deldir 2.0-4 2024-02-28 [1] CRAN (R 4.4.0) #> digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0) #> dotCall64 1.1-1 2023-11-28 [1] CRAN (R 4.4.0) #> dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.0) #> evaluate 0.23 2023-11-01 [1] CRAN (R 4.4.0) #> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0) #> farver 2.1.2 2024-05-13 [1] CRAN (R 4.4.0) #> fastDummies 1.7.3 2023-07-06 [1] CRAN (R 4.4.0) #> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.4.0) #> fitdistrplus 1.1-11 2023-04-25 [1] CRAN (R 4.4.0) #> forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.4.0) #> fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0) #> future 1.33.2 2024-03-26 [1] CRAN (R 4.4.0) #> future.apply 1.11.2 2024-03-28 [1] CRAN (R 4.4.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0) #> GenomeInfoDb 1.40.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) #> GenomeInfoDbData 1.2.12 2024-05-01 [1] Bioconductor #> GenomicRanges 1.56.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.0) #> ggbeeswarm 0.7.2 2023-04-29 [1] CRAN (R 4.4.0) #> ggplot2 * 3.5.1 2024-04-23 [1] CRAN (R 4.4.0) #> ggprism 1.0.5 2024-03-21 [1] CRAN (R 4.4.0) #> ggrastr 1.0.2 2023-06-01 [1] CRAN (R 4.4.0) #> ggrepel 0.9.5 2024-01-10 [1] CRAN (R 4.4.0) #> ggridges 0.5.6 2024-01-23 [1] CRAN (R 4.4.0) #> GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.4.0) #> globals 0.16.3 2024-03-08 [1] CRAN (R 4.4.0) #> glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0) #> goftest 1.2-3 2021-10-07 [1] CRAN (R 4.4.0) #> gridExtra 2.3 2017-09-09 [1] CRAN (R 4.4.0) #> gtable 0.3.5 2024-04-22 [1] CRAN (R 4.4.0) #> highr 0.10 2022-12-22 [1] CRAN (R 4.4.0) #> hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0) #> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0) #> htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0) #> httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0) #> httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0) #> ica 1.0-3 2022-07-08 [1] CRAN (R 4.4.0) #> igraph 2.0.3 2024-03-13 [1] CRAN (R 4.4.0) #> IRanges 2.38.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) #> irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.4.0) #> janitor 2.2.0 2023-02-02 [1] CRAN (R 4.4.0) #> jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.4.0) #> KernSmooth 2.23-22 2023-07-10 [1] CRAN (R 4.4.0) #> knitr 1.46 2024-04-06 [1] CRAN (R 4.4.0) #> ks 1.14.2 2024-01-15 [1] CRAN (R 4.4.0) #> labeling 0.4.3 2023-08-29 [1] CRAN (R 4.4.0) #> later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0) #> lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.0) #> lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.4.0) #> leiden 0.4.3.1 2023-11-17 [1] CRAN (R 4.4.0) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0) #> listenv 0.9.1 2024-01-29 [1] CRAN (R 4.4.0) #> lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.4.0) #> lubridate * 1.9.3 2023-09-27 [1] CRAN (R 4.4.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0) #> MASS 7.3-60.2 2024-04-24 [1] local #> Matrix 1.7-0 2024-03-22 [1] CRAN (R 4.4.0) #> MatrixGenerics 1.16.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) #> matrixStats 1.3.0 2024-04-11 [1] CRAN (R 4.4.0) #> mclust 6.1.1 2024-04-29 [1] CRAN (R 4.4.0) #> mime 0.12 2021-09-28 [1] CRAN (R 4.4.0) #> miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0) #> munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.0) #> mvtnorm 1.2-4 2023-11-27 [1] CRAN (R 4.4.0) #> Nebulosa 1.14.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) #> nlme 3.1-164 2023-11-27 [1] CRAN (R 4.4.0) #> paletteer 1.6.0 2024-01-21 [1] CRAN (R 4.4.0) #> parallelly 1.37.1 2024-02-29 [1] CRAN (R 4.4.0) #> patchwork 1.2.0 2024-01-08 [1] CRAN (R 4.4.0) #> pbapply 1.7-2 2023-06-27 [1] CRAN (R 4.4.0) #> pbmc3k.SeuratData 3.1.4 2024-05-01 [1] local #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0) #> plotly 4.10.4 2024-01-13 [1] CRAN (R 4.4.0) #> plyr 1.8.9 2023-10-02 [1] CRAN (R 4.4.0) #> png 0.1-8 2022-11-29 [1] CRAN (R 4.4.0) #> polyclip 1.10-6 2023-09-27 [1] CRAN (R 4.4.0) #> pracma 2.4.4 2023-11-10 [1] CRAN (R 4.4.0) #> progressr 0.14.0 2023-08-10 [1] CRAN (R 4.4.0) #> promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0) #> purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.4.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.4.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.4.0) #> R.oo 1.26.0 2024-01-24 [1] CRAN (R 4.4.0) #> R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.4.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0) #> RANN 2.6.1 2019-01-08 [1] CRAN (R 4.4.0) #> RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.4.0) #> Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.0) #> RcppAnnoy 0.0.22 2024-01-23 [1] CRAN (R 4.4.0) #> RcppHNSW 0.6.0 2024-02-04 [1] CRAN (R 4.4.0) #> readr * 2.1.5 2024-01-10 [1] CRAN (R 4.4.0) #> rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.4.0) #> reprex 2.1.0 2024-01-11 [1] CRAN (R 4.4.0) #> reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.4.0) #> reticulate 1.36.1 2024-04-22 [1] CRAN (R 4.4.0) #> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0) #> rmarkdown 2.26 2024-03-05 [1] CRAN (R 4.4.0) #> ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.4.0) #> RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.4.0) #> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0) #> Rtsne 0.17 2023-12-07 [1] CRAN (R 4.4.0) #> S4Arrays 1.4.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) #> S4Vectors 0.42.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) #> scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0) #> scattermore 1.2 2023-06-12 [1] CRAN (R 4.4.0) #> scCustomize * 2.1.2.9063 2024-05-10 [1] Github (samuel-marsh/scCustomize@e23ca06) #> sctransform 0.4.1 2023-10-19 [1] CRAN (R 4.4.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0) #> Seurat * 5.1.0 2024-05-10 [1] CRAN (R 4.4.0) #> SeuratObject * 5.0.2 2024-05-08 [1] CRAN (R 4.4.0) #> shape 1.4.6.1 2024-02-23 [1] CRAN (R 4.4.0) #> shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.0) #> SingleCellExperiment 1.26.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) #> snakecase 0.11.1 2023-08-27 [1] CRAN (R 4.4.0) #> sp * 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[hcjarnagin]

Thank you so much for your suggestion! Reverting scCustomize back to 2.0.0 worked. I did have to download XQuartz to my computer and restart R to ensure Cairo was functional, after reverting this package. Thanks again for the great package and the helpful response! Seems to be fully functional now.