How do I remove background from a plot from FeaturePlot function of Seurat 2.3.4

[charlesgwellem]

Hello. I wish to thank you for your work in developing your very efficient and user-friendly package Seurat. To begin I wish to mention that this issue number #1948: Remove background in FeaturePlot has not been able to help me because adding the do.return = TRUE argument does not help the problem.

Inspired by the method in the walk-around function in this post issue #528 , I have successfully plotted the expression of several genes at the same time on my clusters. However I want to remove the default background from the FeaturePlot function by manipulationg the ggplot object that should be returned but I only obtain the same unmodified plot and the value NULL returned when I add additional geom layers.

Seurat::FeaturePlot(object = object, features.plot = "fibrotic.set.score", do.return = T)+ theme_classic()

I get in return the same default plot and NULL returned.

Furthermore, I just noticed that FeaturePlot function in my case returns a list and not a ggplot object.

> class(Seurat::FeaturePlot(nacl_bleo_sub,
+                     features.plot = "fibrotic.set.score",
+                     do.return = T))
[1] "list"

I will be very grateful for any hints to overcome these issues.

session info:

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

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

other attached packages:
 [1] Seurat_2.3.4                DESeq2_1.22.2               forcats_0.4.0               stringr_1.4.0              
 [5] purrr_0.3.2                 readr_1.3.1                 tidyr_0.8.3                 tibble_2.1.3               
 [9] tidyverse_1.2.1             BisqueRNA_1.0               cowplot_1.0.0               SingleCellExperiment_1.4.1 
[13] SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.6         matrixStats_0.54.0         
[17] GenomicRanges_1.34.0        GenomeInfoDb_1.18.2         IRanges_2.16.0              S4Vectors_0.20.1           
[21] xlsx_0.6.1                  openxlsx_4.1.0.1            dplyr_0.8.3                 cellrangerRkit_1.1.0       
[25] Rmisc_1.5                   plyr_1.8.4                  lattice_0.20-35             bit64_0.9-7                
[29] bit_1.1-14                  ggplot2_3.2.0               RColorBrewer_1.1-2          Biobase_2.42.0             
[33] BiocGenerics_0.28.0         Matrix_1.2-14              

loaded via a namespace (and not attached):
  [1] reticulate_1.13        R.utils_2.9.0          tidyselect_0.2.5       RSQLite_2.1.2          AnnotationDbi_1.44.0  
  [6] htmlwidgets_1.3        grid_3.5.1             Rtsne_0.15             munsell_0.5.0          codetools_0.2-15      
 [11] ica_1.0-2              future_1.14.0          withr_2.1.2            colorspace_1.4-1       knitr_1.23            
 [16] rstudioapi_0.10        ROCR_1.0-7             dtw_1.21-3             robustbase_0.93-5      rJava_0.9-11          
 [21] gbRd_0.4-11            listenv_0.7.0          lars_1.2               Rdpack_0.11-0          labeling_0.3          
 [26] GenomeInfoDbData_1.2.0 pheatmap_1.0.12        rhdf5_2.26.2           vctrs_0.2.0            generics_0.0.2        
 [31] xfun_0.8               diptest_0.75-7         R6_2.4.0               rsvd_1.0.2             locfit_1.5-9.1        
 [36] flexmix_2.3-15         hdf5r_1.2.0            bitops_1.0-6           assertthat_0.2.1       SDMTools_1.1-221.1    
 [41] scales_1.0.0           nnet_7.3-12            gtable_0.3.0           npsurv_0.4-0           globals_0.12.4        
 [46] rlang_0.4.0            zeallot_0.1.0          genefilter_1.64.0      splines_3.5.1          lazyeval_0.2.2        
 [51] acepack_1.4.1          broom_0.5.2            checkmate_1.9.4        BiocManager_1.30.4     yaml_2.2.0            
 [56] reshape2_1.4.3         modelr_0.1.4           backports_1.1.4        Hmisc_4.2-0            tools_3.5.1           
 [61] gplots_3.0.1.1         proxy_0.4-23           ggridges_0.5.1         Rcpp_1.0.2             base64enc_0.1-3       
 [66] zlibbioc_1.28.0        RCurl_1.95-4.12        rpart_4.1-13           pbapply_1.4-1          zoo_1.8-6             
 [71] haven_2.1.1            ggrepel_0.8.1          cluster_2.0.7-1        magrittr_1.5           data.table_1.12.2     
 [76] lmtest_0.9-37          RANN_2.6.1             fitdistrplus_1.0-14    hms_0.5.0              xlsxjars_0.6.1        
 [81] lsei_1.2-0             xtable_1.8-4           XML_3.98-1.20          mclust_5.4.5           readxl_1.3.1          
 [86] gridExtra_2.3          compiler_3.5.1         KernSmooth_2.23-15     crayon_1.3.4           R.oo_1.22.0           
 [91] htmltools_0.3.6        segmented_1.0-0        snow_0.4-3             Formula_1.2-3          geneplotter_1.60.0    
 [96] RcppParallel_4.4.3     lubridate_1.7.4        DBI_1.0.0              fpc_2.2-3              MASS_7.3-50           
[101] cli_1.1.0              R.methodsS3_1.7.1      gdata_2.18.0           metap_1.1              igraph_1.2.4.1        
[106] pkgconfig_2.0.2        foreign_0.8-71         plotly_4.9.0           foreach_1.4.7          xml2_1.2.1            
[111] annotate_1.60.1        XVector_0.22.0         bibtex_0.4.2           rvest_0.3.4            digest_0.6.20         
[116] sctransform_0.2.0      RcppAnnoy_0.0.12       tsne_0.1-3             cellranger_1.1.0       leiden_0.3.1          
[121] htmlTable_1.13.1       uwot_0.1.3             kernlab_0.9-27         modeltools_0.2-22      gtools_3.8.1          
[126] nlme_3.1-137           jsonlite_1.6           Rhdf5lib_1.4.3         viridisLite_0.3.0      pillar_1.4.2          
[131] DEoptimR_1.0-8         httr_1.4.0             survival_2.42-3        glue_1.3.1             zip_2.0.3             
[136] prabclus_2.3-1         iterators_1.0.12       png_0.1-7              mixtools_1.1.0         class_7.3-14          
[141] stringi_1.4.3          blob_1.2.0             doSNOW_1.0.18          latticeExtra_0.6-28    caTools_1.17.1.2      
[146] memoise_1.1.0          irlba_2.3.3            future.apply_1.3.0     ape_5.3 

[mojaveazure]

This is a question for Seurat, not SeuratWrappers

[MingBit]

sorry to bring this up again! I am also having hard time to remove the grey background..
It would be great if you could let me know whether you solved the problem...
thanks :D

[MingBit]

hey! I got it.. just add p + theme_set(theme_cowplot()) ..