Cell_Highlight_Plot defaulting to object reduction. New behavior

[zrlewis]

Thanks for a great package @samuel-marsh !

I encountered a potential bug in Cell_Highlight_Plot()

It seems to no longer accept a reduction argument.

MS4A1 <- WhichCells(object = pbmc_small, expression = MS4A1 > 4)
GZMB <- WhichCells(object = pbmc_small, expression = GZMB > 4)

cells <- list("MS4A1" = MS4A1,
              "GZMB" = GZMB)

# default reduction plotted
p1 <- Cell_Highlight_Plot(seurat_object = pbmc_small, cells_highlight = cells)
# specifying reduction does not work below
p2 <- Cell_Highlight_Plot(seurat_object = pbmc_small, cells_highlight = cells, reduction = "pca")
# specifying a reduction still works for DimPlots
p3 <- DimPlot_scCustom(seurat_object = pbmc_small, cells.highlight = cells, reduction = "pca")


p1 / p2 / p3

> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS/LAPACK: /opt/conda/lib/libopenblasp-r0.3.23.so

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

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

other attached packages:
 [1] scCustomize_3.0.0  lubridate_1.9.4    forcats_1.0.0      purrr_1.0.2        readr_2.1.5        tidyr_1.3.1        tibble_3.2.1       tidyverse_2.0.0    patchwork_1.3.0   
[10] uwot_0.2.2         Seurat_5.1.0       SeuratObject_5.0.2 sp_2.1-4           cowplot_1.1.3      Matrix_1.6-5       RColorBrewer_1.1-3 plotly_4.10.4      stringr_1.5.1     
[19] matrixStats_1.4.1  ggplot2_3.5.1      gridExtra_2.3      dplyr_1.1.4        ggsankey_0.0.99999

loaded via a namespace (and not attached):
  [1] spatstat.univar_3.1-1  spam_2.11-0            circlize_0.4.16        systemfonts_1.1.0      plyr_1.8.9             igraph_2.0.3.9038      lazyeval_0.2.2        
  [8] splines_4.2.3          RcppHNSW_0.6.0         listenv_0.9.1          scattermore_1.2        digest_0.6.37          htmltools_0.5.8.1      viridis_0.6.5         
 [15] fansi_1.0.6            magrittr_2.0.3         paletteer_1.6.0        tensor_1.5             cluster_2.1.4          ROCR_1.0-11            tzdb_0.4.0            
 [22] globals_0.16.3         R.utils_2.12.3         svglite_2.1.3          timechange_0.3.0       spatstat.sparse_3.1-0  colorspace_2.1-1       ggrepel_0.9.6         
 [29] textshaping_0.4.1      crayon_1.5.3           prismatic_1.1.2        jsonlite_1.8.9         progressr_0.15.1       spatstat.data_3.1-4    survival_3.5-5        
 [36] zoo_1.8-12             glue_1.8.0             polyclip_1.10-7        gtable_0.3.6           leiden_0.4.3.1         future.apply_1.11.3    shape_1.4.6.1         
 [43] BiocGenerics_0.44.0    abind_1.4-8            scales_1.3.0           spatstat.random_3.3-2  ggthemes_5.1.0         miniUI_0.1.1.1         Rcpp_1.0.13-1         
 [50] viridisLite_0.4.2      xtable_1.8-4           reticulate_1.40.0      dotCall64_1.2          stats4_4.2.3           htmlwidgets_1.6.4      httr_1.4.7            
 [57] ica_1.0-3              R.methodsS3_1.8.2      pkgconfig_2.0.3        farver_2.1.2           deldir_2.0-4           utf8_1.2.4             janitor_2.2.0         
 [64] tidyselect_1.2.1       labeling_0.4.3         rlang_1.1.4            reshape2_1.4.4         later_1.4.1            munsell_0.5.1          tools_4.2.3           
 [71] cli_3.6.3              ggprism_1.0.5          generics_0.1.3         ggridges_0.5.6         fastmap_1.2.0          ragg_1.2.5             goftest_1.2-3         
 [78] rematch2_2.1.2         fitdistrplus_1.2-1     RANN_2.6.2             pbapply_1.7-2          future_1.34.0          nlme_3.1-162           mime_0.12             
 [85] R.oo_1.27.0            ggrastr_1.0.2          compiler_4.2.3         rstudioapi_0.17.1      beeswarm_0.4.0         png_0.1-8              spatstat.utils_3.1-1  
 [92] stringi_1.8.4          RSpectra_0.16-2        lattice_0.21-8         vctrs_0.6.5            pillar_1.9.0           lifecycle_1.0.4        spatstat.geom_3.3-4   
 [99] lmtest_0.9-40          GlobalOptions_0.1.2    RcppAnnoy_0.0.22       data.table_1.16.4      irlba_2.3.5.1          httpuv_1.6.15          R6_2.5.1              
[106] promises_1.3.2         KernSmooth_2.23-22     vipor_0.4.7            parallelly_1.40.1      codetools_0.2-19       fastDummies_1.7.4      MASS_7.3-60           
[113] withr_3.0.2            sctransform_0.4.1      S4Vectors_0.36.2       parallel_4.2.3         hms_1.1.3              grid_4.2.3             snakecase_0.11.1      
[120] Rtsne_0.17             spatstat.explore_3.3-3 shiny_1.9.1            ggbeeswarm_0.7.2      

[samuel-marsh]

Hi @zrlewis,

Thanks for kind words and for finding this bug. I have just fixed it now in the develop branch. I'm aiming for push hotfix to CRAN by end of the week.

Thanks again!
Sam

[zrlewis]

Thanks very much!