plot_median = TRUE does not work in VlnPlot_scCustom when features contains more than one gene
Closed this issue · 1 comments
CroixJeremy2 commented
Hello,
Thanks for all your amazing work!
Everything is in the title. Actually, plot_median = TRUE works but only for the last gene...
Here is a minimal example:
library(Seurat)
library(SeuratData)
library(scCustomize)
data("pbmc3k")
pbmc3k = UpdateSeuratObject(pbmc3k)
pbmc3k = NormalizeData(object = pbmc3k)
pbmc3k = FindVariableFeatures(object = pbmc3k)
pbmc3k = ScaleData(object = pbmc3k)
pbmc3k = RunPCA(object = pbmc3k)
pbmc3k = RunUMAP(object = pbmc3k, dims = 1:20)
pbmc3k = FindNeighbors(object = pbmc3k, dims = 1:20)
pbmc3k = FindClusters(object = pbmc3k, resolution = 0.50)
DimPlot_scCustom(seurat_object = pbmc3k, group.by = "seurat_clusters")
The following code works if only one gene is in feature =
FeaturePlot_scCustom(seurat_object = pbmc3k, features = "GAPDH") /
VlnPlot_scCustom(seurat_object = pbmc3k, group.by = "seurat_clusters", features = "GAPDH", plot_median = TRUE) & NoLegend()
But the following codes do not work if several genes are in feature =
FeaturePlot_scCustom(seurat_object = pbmc3k, features = c("GAPDH", "VIM"), num_columns = 2) /
VlnPlot_scCustom(seurat_object = pbmc3k, group.by = "seurat_clusters", features = c("GAPDH", "VIM"), plot_median = TRUE, num_columns = 2)
FeaturePlot_scCustom(seurat_object = pbmc3k, features = c("GAPDH", "VIM", "RPS18"), num_columns = 3) /
VlnPlot_scCustom(seurat_object = pbmc3k, group.by = "seurat_clusters", features = c("GAPDH", "VIM", "RPS18"), plot_median = TRUE, num_columns = 3)
I tried these codes, but it didn't work... Plus, using these codes, I don't see any median at all in the plots, and no warning in the console.
FeaturePlot_scCustom(seurat_object = pbmc3k, features = c("GAPDH", "VIM"), num_columns = 2) /
VlnPlot_scCustom(seurat_object = pbmc3k, group.by = "seurat_clusters", features = c("GAPDH", "VIM"), plot_median = c(TRUE, TRUE), num_columns = 2)
FeaturePlot_scCustom(seurat_object = pbmc3k, features = c("GAPDH", "VIM"), num_columns = 2) /
VlnPlot_scCustom(seurat_object = pbmc3k, group.by = "seurat_clusters", features = c("GAPDH", "VIM"), plot_median = list(TRUE, TRUE), num_columns = 2)
Thanks in advance for solving this issue,
Best regards,
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.7.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] C
time zone: Europe/Paris
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] scCustomize_2.0.1 pbmc3k.SeuratData_3.1.4 ifnb.SeuratData_3.1.0
[4] SeuratData_0.2.2.9001 Seurat_5.0.1 SeuratObject_5.0.1
[7] sp_2.1-3
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.8 shape_1.4.6
[4] magrittr_2.0.3 spatstat.utils_3.0-4 ggbeeswarm_0.7.2
[7] farver_2.1.1 GlobalOptions_0.1.2 vctrs_0.6.5
[10] ROCR_1.0-11 spatstat.explore_3.2-6 paletteer_1.6.0
[13] janitor_2.2.0 htmltools_0.5.7 forcats_1.0.0
[16] sctransform_0.4.1 parallelly_1.36.0 KernSmooth_2.23-22
[19] htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9
[22] lubridate_1.9.3 plotly_4.10.4 zoo_1.8-12
[25] igraph_2.0.1.1 mime_0.12 lifecycle_1.0.4
[28] pkgconfig_2.0.3 Matrix_1.6-5 R6_2.5.1
[31] fastmap_1.1.1 snakecase_0.11.1 fitdistrplus_1.1-11
[34] future_1.33.1 shiny_1.8.0 digest_0.6.34
[37] colorspace_2.1-0 rematch2_2.1.2 patchwork_1.2.0
[40] tensor_1.5 RSpectra_0.16-1 irlba_2.3.5.1
[43] labeling_0.4.3 progressr_0.14.0 timechange_0.3.0
[46] fansi_1.0.6 spatstat.sparse_3.0-3 httr_1.4.7
[49] polyclip_1.10-6 abind_1.4-5 compiler_4.3.1
[52] withr_3.0.0 fastDummies_1.7.3 MASS_7.3-60.0.1
[55] rappdirs_0.3.3 tools_4.3.1 vipor_0.4.7
[58] lmtest_0.9-40 beeswarm_0.4.0 httpuv_1.6.14
[61] future.apply_1.11.1 goftest_1.2-3 glue_1.7.0
[64] nlme_3.1-164 promises_1.2.1 grid_4.3.1
[67] Rtsne_0.17 cluster_2.1.6 reshape2_1.4.4
[70] generics_0.1.3 gtable_0.3.4 spatstat.data_3.0-4
[73] tidyr_1.3.1 data.table_1.15.0 utf8_1.2.4
[76] spatstat.geom_3.2-8 RcppAnnoy_0.0.22 ggrepel_0.9.5
[79] RANN_2.6.1 pillar_1.9.0 stringr_1.5.1
[82] spam_2.10-0 RcppHNSW_0.6.0 ggprism_1.0.4
[85] later_1.3.2 circlize_0.4.16 splines_4.3.1
[88] dplyr_1.1.4 lattice_0.22-5 survival_3.5-7
[91] deldir_2.0-2 tidyselect_1.2.0 miniUI_0.1.1.1
[94] pbapply_1.7-2 gridExtra_2.3 scattermore_1.2
[97] matrixStats_1.2.0 stringi_1.8.3 lazyeval_0.2.2
[100] codetools_0.2-19 tibble_3.2.1 cli_3.6.2
[103] uwot_0.1.16 xtable_1.8-4 reticulate_1.35.0
[106] munsell_0.5.0 Rcpp_1.0.12 globals_0.16.2
[109] spatstat.random_3.2-2 png_0.1-8 ggrastr_1.0.2
[112] parallel_4.3.1 ellipsis_0.3.2 ggplot2_3.4.4
[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 crayon_1.5.2 rlang_1.1.3
[124] cowplot_1.1.3samuel-marsh commented
Hi @CroixJeremy2,
Thanks for kind words! Thanks for finding bug. I have just fixed this in the develop branch (v2.1.2.9022 or greater). If the issue persists after installing the dev branch please let me know and I'll reopen the issue.
Best,
Sam