"alpha_exp" changing the transparency of the scalebar and not the points.

[ishwarvh]

Hello,
Thank you for this really helpful package. I just noticed that the alpha_exp parameter in the Featureplot_scCustom function is changing the transparency of the scalebar and not the points.

I am using scCustomize-v2.0.1

FeaturePlot_scCustom(pbmc_small, "IL7R", pt.size = 8, alpha_exp = 1)

FeaturePlot_scCustom(pbmc_small, "IL7R", pt.size = 8, alpha_exp = 0.5)

sessionInfo

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

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=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Chicago
tzcode source: system (glibc)

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

other attached packages:
 [1] plot3D_1.4               rgl_1.2.1                harmony_1.1.0            Rcpp_1.0.11              BPCells_0.1.0            scCustomize_2.0.1        reticulate_1.34.0        patchwork_1.1.3         
 [9] ggplot2_3.4.4            Azimuth_0.5.0            shinyBS_0.61.1           SeuratWrappers_0.3.2     pbmcsca.SeuratData_3.0.0 SeuratData_0.2.2.9001    Seurat_5.0.1             SeuratObject_5.0.1      
[17] sp_2.1-1                

loaded via a namespace (and not attached):
  [1] IRanges_2.36.0                    R.methodsS3_1.8.2                 progress_1.2.2                    poweRlaw_0.70.6                   goftest_1.2-3                     DT_0.30                          
  [7] Biostrings_2.70.1                 vctrs_0.6.4                       spatstat.random_3.2-1             digest_0.6.33                     png_0.1-8                         shape_1.4.6                      
 [13] ggrepel_0.9.4                     deldir_1.0-9                      parallelly_1.36.0                 renv_1.0.3                        MASS_7.3-60                       Signac_1.12.0                    
 [19] reshape2_1.4.4                    httpuv_1.6.12                     BiocGenerics_0.48.1               withr_2.5.2                       ggrastr_1.0.2                     xfun_0.41                        
 [25] ellipsis_0.3.2                    survival_3.5-7                    EnsDb.Hsapiens.v86_2.99.0         memoise_2.0.1                     ggbeeswarm_0.7.2                  janitor_2.2.0                    
 [31] systemfonts_1.0.5                 ragg_1.2.6                        zoo_1.8-12                        GlobalOptions_0.1.2               gtools_3.9.4                      pbapply_1.7-2                    
 [37] R.oo_1.25.0                       prettyunits_1.2.0                 rematch2_2.1.2                    KEGGREST_1.42.0                   promises_1.2.1                    httr_1.4.7                       
 [43] restfulr_0.0.15                   globals_0.16.2                    fitdistrplus_1.1-11               rhdf5filters_1.14.1               rhdf5_2.46.0                      rstudioapi_0.15.0                
 [49] miniUI_0.1.1.1                    generics_0.1.3                    base64enc_0.1-3                   curl_5.1.0                        S4Vectors_0.40.1                  zlibbioc_1.48.0                  
 [55] polyclip_1.10-6                   GenomeInfoDbData_1.2.11           SparseArray_1.2.2                 xtable_1.8-4                      stringr_1.5.1                     pracma_2.4.4                     
 [61] S4Arrays_1.2.0                    BiocFileCache_2.10.1              hms_1.1.3                         GenomicRanges_1.54.1              irlba_2.3.5.1                     colorspace_2.1-0                 
 [67] filelock_1.0.2                    hdf5r_1.3.8                       ROCR_1.0-11                       spatstat.data_3.0-3               magrittr_2.0.3                    lmtest_0.9-40                    
 [73] snakecase_0.11.1                  readr_2.1.4                       misc3d_0.9-1                      later_1.3.1                       lattice_0.22-5                    glmGamPoi_1.14.0                 
 [79] spatstat.geom_3.2-7               future.apply_1.11.0               scattermore_1.2                   XML_3.99-0.15                     cowplot_1.1.1                     matrixStats_1.1.0                
 [85] RcppAnnoy_0.0.21                  pillar_1.9.0                      nlme_3.1-163                      caTools_1.18.2                    compiler_4.3.2                    RSpectra_0.16-1                  
 [91] stringi_1.8.1                     tensor_1.5                        SummarizedExperiment_1.32.0       lubridate_1.9.3                   GenomicAlignments_1.38.0          plyr_1.8.9                       
 [97] crayon_1.5.2                      abind_1.4-5                       BiocIO_1.12.0                     googledrive_2.1.1                 bit_4.0.5                         dplyr_1.1.4                      
[103] fastmatch_1.1-4                   codetools_0.2-19                  textshaping_0.3.7                 paletteer_1.5.0                   plotly_4.10.3                     mime_0.12                        
[109] splines_4.3.2                     circlize_0.4.15                   fastDummies_1.7.3                 dbplyr_2.4.0                      sparseMatrixStats_1.14.0          prismatic_1.1.1                  
[115] cellranger_1.1.0                  knitr_1.45                        blob_1.2.4                        utf8_1.2.4                        seqLogo_1.68.0                    AnnotationFilter_1.26.0          
[121] fs_1.6.3                          listenv_0.9.0                     DelayedMatrixStats_1.24.0         tibble_3.2.1                      Matrix_1.6-3                      tzdb_0.4.0                       
[127] pkgconfig_2.0.3                   tools_4.3.2                       cachem_1.0.8                      RhpcBLASctl_0.23-42               RSQLite_2.3.3                     viridisLite_0.4.2                
[133] DBI_1.1.3                         fastmap_1.1.1                     scales_1.2.1                      grid_4.3.2                        ica_1.0-3                         shinydashboard_0.7.2             
[139] Rsamtools_2.18.0                  ggprism_1.0.4                     BiocManager_1.30.22               dotCall64_1.1-0                   RANN_2.6.1                        farver_2.1.1                     
[145] yaml_2.3.7                        MatrixGenerics_1.14.0             rtracklayer_1.62.0                cli_3.6.1                         purrr_1.0.2                       stats4_4.3.2                     
[151] leiden_0.4.3                      lifecycle_1.0.4                   uwot_0.1.16                       Biobase_2.62.0                    presto_1.0.0                      BSgenome.Hsapiens.UCSC.hg38_1.4.5
[157] BiocParallel_1.36.0               annotate_1.80.0                   timechange_0.2.0                  gtable_0.3.4                      rjson_0.2.21                      ggridges_0.5.4                   
[163] progressr_0.14.0                  parallel_4.3.2                    jsonlite_1.8.7                    RcppHNSW_0.5.0                    TFBSTools_1.40.0                  bitops_1.0-7                     
[169] bit64_4.0.5                       Rtsne_0.16                        spatstat.utils_3.0-4              CNEr_1.38.0                       shinyjs_2.1.0                     SeuratDisk_0.0.0.9021            
[175] R.utils_2.12.2                    lazyeval_0.2.2                    shiny_1.7.5.1                     htmltools_0.5.7                   GO.db_3.18.0                      sctransform_0.4.1                
[181] rappdirs_0.3.3                    ensembldb_2.26.0                  glue_1.6.2                        tcltk_4.3.2                       TFMPvalue_0.0.9                   spam_2.10-0                      
[187] googlesheets4_1.1.1               XVector_0.42.0                    RCurl_1.98-1.13                   BSgenome_1.70.1                   gridExtra_2.3                     JASPAR2020_0.99.10               
[193] igraph_1.5.1                      R6_2.5.1                          tidyr_1.3.0                       forcats_1.0.0                     RcppRoll_0.3.0                    labeling_0.4.3                   
[199] GenomicFeatures_1.54.1            cluster_2.1.4                     Rhdf5lib_1.24.0                   gargle_1.5.2                      GenomeInfoDb_1.38.1               DirichletMultinomial_1.44.0      
[205] DelayedArray_0.28.0               tidyselect_1.2.0                  vipor_0.4.5                       ProtGenerics_1.34.0               xml2_1.3.5                        AnnotationDbi_1.64.1             
[211] future_1.33.0                     rsvd_1.0.5                        munsell_0.5.0                     KernSmooth_2.23-22                data.table_1.14.8                 htmlwidgets_1.6.2                
[217] RColorBrewer_1.1-3                biomaRt_2.58.0                    rlang_1.1.2                       spatstat.sparse_3.0-3             spatstat.explore_3.2-5            remotes_2.4.2.1                  
[223] fansi_1.0.5                       beeswarm_0.4.0                   

[samuel-marsh]

Hi @ishwarvh,

Thanks for kind words and thanks for pointing this out. I think when the update to V5 added alpha as true parameter this may have stopped working correctly. I’ll push update when I can this week to do version check and pass parameter appropriately. I’ll post again when all set.

Best,
Sam

[samuel-marsh]

Hi @ishwarvh,

This should be all set now on develop branch (v2.0.1.9009). If issue still persists after updating to this version please let me know and I'll reopen the issue.

Best,
Sam

[ishwarvh]

Thank you for the fix. Can confirm it works as expected now.

Ishwar