only one scale legend appears when splited by condition

[dahun73]

Hello everyone :)

I have a question about showing feature plot.
When I use 'split.by' parameter, only one scale legend is shown like this.

I want to show scale legend with all genes. How can I fix it?

Thank you in advance!

Dahun

pdf("Featureplot_inte.combined_list_split_cluster_220110.pdf",height =20,width = 10)
FeaturePlot(inte.combined.1,features = c("Eomes","Pax6","Tbr1","Sox2","Tubb3","Rbfox3","Bcl11b","Cux1"),split.by = "stim",reduction = 'umap',keep.scale = 'all',label = "TRUE")+theme(legend.position = "right")
dev.off()

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 21.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=ko_KR.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=ko_KR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=ko_KR.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=ko_KR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ggrepel_0.9.1               ggfortify_0.4.13            SCINA_1.2.0                
 [4] gplots_3.1.1                MASS_7.3-54                 metap_1.5                  
 [7] multtest_2.48.0             SeuratObject_4.0.2          Seurat_4.0.5               
[10] devtools_2.4.2              usethis_2.1.3               scRNAseq_2.6.1             
[13] RColorBrewer_1.1-2          pheatmap_1.0.12             SingleR_1.6.1              
[16] celldex_1.2.0               SingleCellExperiment_1.14.1 SummarizedExperiment_1.22.0
[19] Biobase_2.52.0              GenomicRanges_1.44.0        GenomeInfoDb_1.28.4        
[22] IRanges_2.26.0              S4Vectors_0.30.2            BiocGenerics_0.38.0        
[25] MatrixGenerics_1.4.3        matrixStats_0.61.0          ggpubr_0.4.0               
[28] ggsignif_0.6.3              ggplot2_3.3.5               cowplot_1.1.1              
[31] patchwork_1.1.1             dplyr_1.0.7                

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3                rtracklayer_1.52.1            scattermore_0.7              
  [4] tidyr_1.1.4                   bit64_4.0.5                   multcomp_1.4-17              
  [7] irlba_2.3.3                   DelayedArray_0.18.0           rpart_4.1-15                 
 [10] data.table_1.14.2             KEGGREST_1.32.0               RCurl_1.98-1.5               
 [13] AnnotationFilter_1.16.0       generics_0.1.1                GenomicFeatures_1.44.2       
 [16] ScaledMatrix_1.0.0            TH.data_1.1-0                 callr_3.7.0                  
 [19] RSQLite_2.2.8                 RANN_2.6.1                    future_1.23.0                
 [22] bit_4.0.4                     mutoss_0.1-12                 spatstat.data_2.1-0          
 [25] xml2_1.3.2                    httpuv_1.6.3                  assertthat_0.2.1             
 [28] xfun_0.27                     hms_1.1.1                     promises_1.2.0.1             
 [31] fansi_0.5.0                   restfulr_0.0.13               progress_1.2.2               
 [34] caTools_1.18.2                dbplyr_2.1.1                  readxl_1.3.1                 
 [37] tmvnsim_1.0-2                 igraph_1.2.7                  DBI_1.1.1                    
 [40] htmlwidgets_1.5.4             spatstat.geom_2.3-0           purrr_0.3.4                  
 [43] ellipsis_0.3.2                backports_1.3.0               biomaRt_2.48.3               
 [46] deldir_1.0-6                  sparseMatrixStats_1.4.2       vctrs_0.3.8                  
 [49] remotes_2.4.1                 ensembldb_2.16.4              ROCR_1.0-11                  
 [52] abind_1.4-5                   cachem_1.0.6                  withr_2.4.2                  
 [55] sctransform_0.3.2             GenomicAlignments_1.28.0      prettyunits_1.1.1            
 [58] mnormt_2.0.2                  goftest_1.2-3                 cluster_2.1.2                
 [61] ExperimentHub_2.0.0           lazyeval_0.2.2                crayon_1.4.2                 
 [64] labeling_0.4.2                pkgconfig_2.0.3               nlme_3.1-153                 
 [67] pkgload_1.2.3                 ProtGenerics_1.24.0           rlang_0.4.12                 
 [70] globals_0.14.0                lifecycle_1.0.1               miniUI_0.1.1.1               
 [73] sandwich_3.0-1                filelock_1.0.2                BiocFileCache_2.0.0          
 [76] mathjaxr_1.4-0                rsvd_1.0.5                    AnnotationHub_3.0.2          
 [79] cellranger_1.1.0              rprojroot_2.0.2               polyclip_1.10-0              
 [82] lmtest_0.9-38                 Matrix_1.4-0                  carData_3.0-4                
 [85] zoo_1.8-9                     ggridges_0.5.3                processx_3.5.2               
 [88] png_0.1-7                     viridisLite_0.4.0             rjson_0.2.20                 
 [91] bitops_1.0-7                  KernSmooth_2.23-20            Biostrings_2.60.2            
 [94] blob_1.2.2                    DelayedMatrixStats_1.14.3     stringr_1.4.0                
 [97] parallelly_1.28.1             rstatix_0.7.0                 beachmat_2.8.1               
[100] scales_1.1.1                  memoise_2.0.0                 magrittr_2.0.1               
[103] plyr_1.8.6                    ica_1.0-2                     zlibbioc_1.38.0              
[106] compiler_4.1.2                tinytex_0.34                  BiocIO_1.2.0                 
[109] plotrix_3.8-2                 fitdistrplus_1.1-6            Rsamtools_2.8.0              
[112] cli_3.1.0                     XVector_0.32.0                listenv_0.8.0                
[115] pbapply_1.5-0                 ps_1.6.0                      mgcv_1.8-38                  
[118] tidyselect_1.1.1              stringi_1.7.5                 forcats_0.5.1                
[121] yaml_2.2.1                    BiocSingular_1.8.1            grid_4.1.2                   
[124] tools_4.1.2                   future.apply_1.8.1            rio_0.5.27                   
[127] rstudioapi_0.13               foreign_0.8-81                gridExtra_2.3                
[130] farver_2.1.0                  Rtsne_0.15                    digest_0.6.28                
[133] BiocManager_1.30.16           shiny_1.7.1                   Rcpp_1.0.7                   
[136] car_3.0-11                    broom_0.7.10                  BiocVersion_3.13.1           
[139] later_1.3.0                   RcppAnnoy_0.0.19              httr_1.4.2                   
[142] AnnotationDbi_1.54.1          Rdpack_2.1.2                  colorspace_2.0-2             
[145] XML_3.99-0.8                  fs_1.5.0                      tensor_1.5                   
[148] reticulate_1.22               splines_4.1.2                 uwot_0.1.10                  
[151] sn_2.0.0                      spatstat.utils_2.2-0          plotly_4.10.0                
[154] sessioninfo_1.2.0             xtable_1.8-4                  jsonlite_1.7.2               
[157] testthat_3.1.0                R6_2.5.1                      TFisher_0.2.0                
[160] pillar_1.6.4                  htmltools_0.5.2               mime_0.12                    
[163] glue_1.5.0                    fastmap_1.1.0                 BiocParallel_1.26.2          
[166] BiocNeighbors_1.10.0          interactiveDisplayBase_1.30.0 codetools_0.2-18             
[169] mvtnorm_1.1-3                 pkgbuild_1.2.0                utf8_1.2.2                   
[172] lattice_0.20-45               spatstat.sparse_2.0-0         tibble_3.1.6                 
[175] numDeriv_2016.8-1.1           curl_4.3.2                    leiden_0.3.9                 
[178] gtools_3.9.2                  zip_2.2.0                     openxlsx_4.2.4               
[181] survival_3.2-13               desc_1.4.0                    munsell_0.5.0                
[184] GenomeInfoDbData_1.2.6        haven_2.4.3                   reshape2_1.4.4               
[187] gtable_0.3.0                  rbibutils_2.2.4               spatstat.core_2.3-0

[samuel-marsh]

Hi,

Not member of dev team but hopefully can be helpful. This is because layout plots use the patchwork package. To add legend simply use FeaturePlot(...) & theme(legend.position = "right") to show all legends.

Also as FYI currently in Seurat there is bug with displaying the plots using the same scale when using split.by. If you want to display all plots split.by you can use FeaturePlot_scCustom from the scCustomize package. See #5243 (comment) for more info.

Best,
Sam

[dahun73]

Hi,

Not member of dev team but hopefully can be helpful. This is because layout plots use the patchwork package. To add legend simply use FeaturePlot(...) & theme(legend.position = "right") to show all legends.

Also as FYI currently in Seurat there is bug with displaying the plots using the same scale when using split.by. If you want to display all plots split.by you can use FeaturePlot_scCustom from the scCustomize package. See #5243 (comment) for more info.

Best, Sam

Dear Sam,

Thank you so much.

Because I used '+ theme', only last one have scale legend.
Have a good day! :)

Dahun