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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Colors not changing with DEenrichRPlot plot #9066

Open KatGoldfinch opened 3 months ago

KatGoldfinch commented 3 months ago

Trying to change colors in the DEenrichRPlot plot with the "col" argument, but it does not work 

DEenrichRPlot(Seurat_object, ident.1 = "KO", ident.2 = "WT", max.genes = 300, enrich.database = "Transcription_Factor_PPIs", p.val.cutoff=0.05,num.pathway  =25, logfc.threshold=0.3, cols = c("#ed00b7", "#00dcff") )

image

sessionInfo() R version 4.4.0 (2024-04-24) Platform: x86_64-pc-linux-gnu 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
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Warsaw tzcode source: system (glibc)

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

other attached packages: [1] dplyr_1.1.4 Seurat_5.0.3 ggplot2_3.5.1 SeuratObject_5.0.1 sp_2.1-4 enrichR_3.2

loaded via a namespace (and not attached): [1] GSVA_1.52.0 fs_1.6.4 matrixStats_1.3.0 spatstat.sparse_3.0-3
[5] lubridate_1.9.3 devtools_2.4.5 httr_1.4.7 RColorBrewer_1.1-3
[9] doParallel_1.0.17 profvis_0.3.8 tools_4.4.0 sctransform_0.4.1
[13] utf8_1.2.4 R6_2.5.1 HDF5Array_1.32.0 ggdist_3.3.2
[17] lazyeval_0.2.2 uwot_0.2.2 mgcv_1.9-1 rhdf5filters_1.16.0
[21] GetoptLong_1.0.5 urlchecker_1.0.1 withr_3.0.0 scCustomize_2.1.2
[25] gridExtra_2.3 progressr_0.14.0 cli_3.6.2 Biobase_2.64.0
[29] spatstat.explore_3.2-7 fastDummies_1.7.3 labeling_0.4.3 sass_0.4.9
[33] dittoSeq_1.16.0 spatstat.data_3.0-4 ggridges_0.5.6 pbapply_1.7-2
[37] R.utils_2.12.3 parallelly_1.37.1 WriteXLS_6.5.0 sessioninfo_1.2.2
[41] limma_3.60.0 readxl_1.4.3 rstudioapi_0.16.0 RSQLite_2.3.6
[45] shape_1.4.6.1 generics_0.1.3 ica_1.0-3 spatstat.random_3.2-3
[49] distributional_0.4.0 Matrix_1.7-0 ggbeeswarm_0.7.2 fansi_1.0.6
[53] S4Vectors_0.42.0 abind_1.4-5 R.methodsS3_1.8.2 lifecycle_1.0.4
[57] yaml_2.3.8 snakecase_0.11.1 SummarizedExperiment_1.34.0 rhdf5_2.48.0
[61] SparseArray_1.4.0 Rtsne_0.17 paletteer_1.6.0 grid_4.4.0
[65] blob_1.2.4 promises_1.3.0 crayon_1.5.2 miniUI_0.1.1.1
[69] lattice_0.22-6 msigdbr_7.5.1 beachmat_2.20.0 cowplot_1.1.3
[73] annotate_1.82.0 KEGGREST_1.44.0 magick_2.8.3 pillar_1.9.0
[77] knitr_1.46 ComplexHeatmap_2.20.0 GenomicRanges_1.56.0 rjson_0.2.21
[81] boot_1.3-30 future.apply_1.11.2 codetools_0.2-20 leiden_0.4.3.1
[85] glue_1.7.0 data.table_1.15.4 remotes_2.5.0 vctrs_0.6.5
[89] png_0.1-8 spam_2.10-0 cellranger_1.1.0 gtable_0.3.5
[93] rematch2_2.1.2 cachem_1.0.8 xfun_0.43 S4Arrays_1.4.0
[97] mime_0.12 survival_3.6-4 DElegate_1.2.1 SingleCellExperiment_1.26.0 [101] pheatmap_1.0.12 iterators_1.0.14 statmod_1.5.0 ellipsis_0.3.2
[105] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-164 usethis_2.2.3
[109] bit64_4.0.5 RcppAnnoy_0.0.22 GenomeInfoDb_1.40.0 bslib_0.7.0
[113] irlba_2.3.5.1 vipor_0.4.7 KernSmooth_2.23-22 colorspace_2.1-0
[117] BiocGenerics_0.50.0 DBI_1.2.2 ggrastr_1.0.2 UCell_2.8.0
[121] tidyselect_1.2.1 bit_4.0.5 compiler_4.4.0 curl_5.2.1
[125] AUCell_1.26.0 graph_1.82.0 BiocNeighbors_1.22.0 DelayedArray_0.30.0
[129] plotly_4.10.4 scales_1.3.0 lmtest_0.9-40 SpatialExperiment_1.14.0
[133] stringr_1.5.1 digest_0.6.35 goftest_1.2-3 presto_1.0.0
[137] spatstat.utils_3.0-4 minqa_1.2.6 rmarkdown_2.26 XVector_0.44.0
[141] decoupleR_2.9.7 htmltools_0.5.8.1 pkgconfig_2.0.3 lme4_1.1-35.3
[145] sparseMatrixStats_1.16.0 MatrixGenerics_1.16.0 fastmap_1.1.1 rlang_1.1.3
[149] GlobalOptions_0.1.2 htmlwidgets_1.6.4 UCSC.utils_1.0.0 shiny_1.8.1.1
[153] DelayedMatrixStats_1.26.0 farver_2.1.1 jquerylib_0.1.4 zoo_1.8-12
[157] jsonlite_1.8.8 BiocParallel_1.38.0 R.oo_1.26.0 BiocSingular_1.20.0
[161] magrittr_2.0.3 GenomeInfoDbData_1.2.12 dotCall64_1.1-1 patchwork_1.2.0
[165] Rhdf5lib_1.26.0 munsell_0.5.1 Rcpp_1.0.12 babelgene_22.9
[169] viridis_0.6.5 reticulate_1.36.1 escape_2.0.0 stringi_1.8.3
[173] zlibbioc_1.50.0 MASS_7.3-60.2 plyr_1.8.9 pkgbuild_1.4.4
[177] parallel_4.4.0 listenv_0.9.1 ggrepel_0.9.5 forcats_1.0.0
[181] deldir_2.0-4 Biostrings_2.72.0 splines_4.4.0 tensor_1.5
[185] circlize_0.4.16 igraph_2.0.3 spatstat.geom_3.2-9 RcppHNSW_0.6.0
[189] ScaledMatrix_1.12.0 reshape2_1.4.4 stats4_4.4.0 pkgload_1.3.4
[193] XML_3.99-0.16.1 evaluate_0.23 BiocManager_1.30.23 ggprism_1.0.5
[197] nloptr_2.0.3 foreach_1.5.2 httpuv_1.6.15 RANN_2.6.1
[201] tidyr_1.3.1 purrr_1.0.2 polyclip_1.10-6 clue_0.3-65
[205] future_1.33.2 scattermore_1.2 janitor_2.2.0 rsvd_1.0.5
[209] xtable_1.8-4 monocle3_1.3.6 RSpectra_0.16-1 later_1.3.2
[213] ggpointdensity_0.1.0 viridisLite_0.4.2 tibble_3.2.1 beeswarm_0.4.0
[217] memoise_2.0.1 AnnotationDbi_1.66.0 IRanges_2.38.0 writexl_1.5.0
[221] cluster_2.1.6 timechange_0.3.0 globals_0.16.3 GSEABase_1.66.0

longmanz commented 2 months ago

Hi, Thank you for reporting this. This is a bug in DEenrichPlot where the cols are directly set to "dodgerblue" and "indianred2". We will try to fix it and get back to you.