Adjusting font size with theme() does not work with figure_plot = TRUE

[wendelljpereira]

Hi @samuel-marsh, thank you for the excellent package !! I really enjoy the enhanced plots.

I am trying to adjust the font size of a DimPlot_scCustom() using theme(). It works as expected when figure_plot = FALSE but does not work properly when figure_plot = TRUE. I fear the same issue is happening with any plot that allows figure_plot = TRUE.

Here is a reproducible example:

require(Seurat)
require(scCustomize)
require(ggplot2)

A <- DimPlot_scCustom(seurat_object = pbmc_small,
                 figure_plot = TRUE)

B <- DimPlot_scCustom(seurat_object = pbmc_small,
                     figure_plot = F) + 
    theme(
        axis.title = element_text(size = 40),
        axis.text = element_text(size = 40),
        legend.text = element_text(size = 40), 
        plot.title = element_blank())

C <- DimPlot_scCustom(seurat_object = pbmc_small,
                      figure_plot = TRUE)+ 
    theme(
        axis.title = element_text(size = 40),
        axis.text = element_text(size = 40),
        legend.text = element_text(size = 40), 
        plot.title = element_blank())


A | B | C

Which produces the image below.

A similar issue happens when I try to replace other aspects of the plot with theme(). For example,

DimPlot_scCustom(seurat_object = pbmc_small,
                      figure_plot = TRUE) + DarkTheme()

Will produce the plot below:

Is there a way to control the aspects of the plot when using figure_plot = TRUE?

sessionInfo() output

R Under development (unstable) (2023-03-29 r84123)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4/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/New_York
tzcode source: internal

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

other attached packages:
[1] ggplot2_3.5.1      scCustomize_2.1.2  Seurat_5.1.0       SeuratObject_5.0.2
[5] sp_2.1-4          

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     rstudioapi_0.16.0      jsonlite_1.8.8        
  [4] shape_1.4.6.1          magrittr_2.0.3         spatstat.utils_3.0-5  
  [7] ggbeeswarm_0.7.2       farver_2.1.2           GlobalOptions_0.1.2   
 [10] vctrs_0.6.5            ROCR_1.0-11            spatstat.explore_3.3-1
 [13] paletteer_1.6.0        janitor_2.2.0          htmltools_0.5.8.1     
 [16] forcats_1.0.0          sctransform_0.4.1      parallelly_1.37.1     
 [19] KernSmooth_2.23-24     htmlwidgets_1.6.4      ica_1.0-3             
 [22] plyr_1.8.9             plotly_4.10.4          zoo_1.8-12            
 [25] lubridate_1.9.3        igraph_2.0.3           mime_0.12             
 [28] lifecycle_1.0.4        pkgconfig_2.0.3        Matrix_1.6-4          
 [31] R6_2.5.1               fastmap_1.2.0          fitdistrplus_1.2-1    
 [34] future_1.33.2          shiny_1.9.1            snakecase_0.11.1      
 [37] digest_0.6.36          colorspace_2.1-1       rematch2_2.1.2        
 [40] patchwork_1.2.0        tensor_1.5             prismatic_1.1.2       
 [43] RSpectra_0.16-2        irlba_2.3.5.1          labeling_0.4.3        
 [46] progressr_0.14.0       fansi_1.0.6            spatstat.sparse_3.1-0 
 [49] timechange_0.3.0       httr_1.4.7             polyclip_1.10-7       
 [52] abind_1.4-5            compiler_4.4.0         withr_3.0.1           
 [55] fastDummies_1.7.3      MASS_7.3-61            tools_4.4.0           
 [58] vipor_0.4.7            lmtest_0.9-40          beeswarm_0.4.0        
 [61] httpuv_1.6.15          future.apply_1.11.2    goftest_1.2-3         
 [64] glue_1.7.0             nlme_3.1-165           promises_1.3.0        
 [67] grid_4.4.0             Rtsne_0.17             cluster_2.1.6         
 [70] reshape2_1.4.4         generics_0.1.3         gtable_0.3.5          
 [73] spatstat.data_3.1-2    tidyr_1.3.1            data.table_1.15.4     
 [76] utf8_1.2.4             spatstat.geom_3.3-2    RcppAnnoy_0.0.22      
 [79] ggrepel_0.9.5          RANN_2.6.1             pillar_1.9.0          
 [82] stringr_1.5.1          spam_2.10-0            RcppHNSW_0.6.0        
 [85] ggprism_1.0.5          later_1.3.2            circlize_0.4.16       
 [88] splines_4.4.0          dplyr_1.1.4            lattice_0.22-6        
 [91] survival_3.7-0         deldir_2.0-4           tidyselect_1.2.1      
 [94] miniUI_0.1.1.1         pbapply_1.7-2          gridExtra_2.3         
 [97] scattermore_1.2        matrixStats_1.3.0      stringi_1.8.4         
[100] lazyeval_0.2.2         codetools_0.2-20       tibble_3.2.1          
[103] cli_3.6.3              uwot_0.2.2             xtable_1.8-4          
[106] reticulate_1.38.0      munsell_0.5.1          Rcpp_1.0.12           
[109] globals_0.16.3         spatstat.random_3.3-1  png_0.1-8             
[112] ggrastr_1.0.2          spatstat.univar_3.0-0  parallel_4.4.0        
[115] dotCall64_1.1-1        listenv_0.9.1          viridisLite_0.4.2     
[118] scales_1.3.0           ggridges_0.5.6         leiden_0.4.3.1        
[121] purrr_1.0.2            rlang_1.1.4            cowplot_1.1.3 

Thank you!
Wendell

[samuel-marsh]

Hi Wendell,

Sorry for the delay getting back to you. Thanks for bringing up the issue. The reason this is happening is because the UMAP axes added by figure_plot are actually a second ggplot2 object and then it is patchwork’ed together. If you use patchwork & instead of ggplot2 + does that resolve the issue?

Best,
Sam