junjunlab/scRNAtoolVis

jjVolcano: This palatte have 12 colors!

CJ-Liu opened this issue · 2 comments

CJ-Liu commented

Dear @junjunlab thanks for your great package. When I used jjVolcano function with demo pbmc data, it encountered the following error, could you give some suggestions to fix the problem, thanks a lot.

jjVolcano(diffData = pbmc.markers)

This palatte have 12 colors!

Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
ERROR while rich displaying an object: Error in palette():
! Insufficient values in manual scale. 15 needed but only 9 provided.

Traceback:

  1. tryCatch(withCallingHandlers({
    . if (!mime %in% names(repr::mime2repr))
    . stop("No repr_* for mimetype ", mime, " in repr::mime2repr")
    . rpr <- repr::mime2repr[mime]
    . if (is.null(rpr))
    . return(NULL)
    . prepare_content(is.raw(rpr), rpr)
    . }, error = error_handler), error = outer_handler)
  2. tryCatchList(expr, classes, parentenv, handlers)
  3. tryCatchOne(expr, names, parentenv, handlers[[1L]])
  4. doTryCatch(return(expr), name, parentenv, handler)
  5. withCallingHandlers({
    . if (!mime %in% names(repr::mime2repr))
    . stop("No repr_* for mimetype ", mime, " in repr::mime2repr")
    . rpr <- repr::mime2repr[mime]
    . if (is.null(rpr))
    . return(NULL)
    . prepare_content(is.raw(rpr), rpr)
    . }, error = error_handler)
  6. repr::mime2repr[mime]
  7. repr_text.default(obj)
  8. paste(capture.output(print(obj)), collapse = "\n")
  9. capture.output(print(obj))
  10. withVisible(...elt(i))
  11. print(obj)
  12. print.ggplot(obj)
  13. ggplot_build(x)
  14. ggplot_build.ggplot(x)
  15. lapply(data, scales_map_df, scales = npscales)
  16. FUN(X[[i]], ...)
  17. unlist(lapply(scales$scales, function(scale) scale$map_df(df = df)),
    . recursive = FALSE)
  18. lapply(scales$scales, function(scale) scale$map_df(df = df))
  19. FUN(X[[i]], ...)
  20. scale$map_df(df = df)
  21. map_df(..., self = self)
  22. lapply(aesthetics, function(j) self$map(df[[j]]))
  23. FUN(X[[i]], ...)
  24. self$map(df[[j]])
  25. map(..., self = self)
  26. self$palette(n)
  27. palette(...)
  28. cli::cli_abort("Insufficient values in manual scale. {n} needed but only {length(values)} provided.")
  29. rlang::abort(message, ..., call = call, use_cli_format = TRUE,
    . .frame = .frame)
  30. signal_abort(cnd, .file)
    ​

sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /opt/conda/lib/libopenblasp-r0.3.21.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] ComplexHeatmap_2.10.0 ggalluvial_0.12.5 corrplot_0.92
[4] scRNAtoolVis_0.0.7 lubridate_1.9.3 forcats_1.0.0
[7] stringr_1.5.1 purrr_1.0.2 readr_2.1.4
[10] tidyr_1.3.0 tibble_3.2.1 tidyverse_2.0.0
[13] RColorBrewer_1.1-3 repr_1.1.4 dplyr_1.1.4
[16] ggplot2_3.4.4 Seurat_5.0.1 SeuratObject_5.0.1
[19] sp_2.1-2

loaded via a namespace (and not attached):
[1] circlize_0.4.15 uuid_1.1-1 spam_2.10-0
[4] plyr_1.8.9 igraph_1.6.0 jjAnno_0.0.3
[7] lazyeval_0.2.2 splines_4.1.3 RcppHNSW_0.5.0
[10] listenv_0.9.0 scattermore_1.2 digest_0.6.33
[13] foreach_1.5.2 htmltools_0.5.7 fansi_1.0.6
[16] magrittr_2.0.3 tensor_1.5 cluster_2.1.4
[19] doParallel_1.0.17 ROCR_1.0-11 tzdb_0.4.0
[22] globals_0.16.2 matrixStats_1.2.0 timechange_0.2.0
[25] spatstat.sparse_3.0-3 colorspace_2.1-0 ggrepel_0.9.4
[28] crayon_1.5.2 jsonlite_1.8.8 progressr_0.14.0
[31] spatstat.data_3.0-3 survival_3.4-0 zoo_1.8-12
[34] iterators_1.0.14 glue_1.6.2 polyclip_1.10-4
[37] gtable_0.3.4 leiden_0.4.3.1 GetoptLong_1.0.5
[40] shape_1.4.6 future.apply_1.11.0 BiocGenerics_0.40.0
[43] abind_1.4-5 scales_1.3.0 spatstat.random_3.2-2
[46] miniUI_0.1.1.1 Rcpp_1.0.11 viridisLite_0.4.2
[49] xtable_1.8-4 clue_0.3-64 reticulate_1.34.0
[52] dotCall64_1.1-1 stats4_4.1.3 htmlwidgets_1.6.4
[55] httr_1.4.7 ellipsis_0.3.2 ica_1.0-3
[58] farver_2.1.1 pkgconfig_2.0.3 uwot_0.1.16
[61] deldir_2.0-2 utf8_1.2.4 labeling_0.4.3
[64] tidyselect_1.2.0 rlang_1.1.2 reshape2_1.4.4
[67] later_1.3.2 munsell_0.5.0 tools_4.1.3
[70] cli_3.6.2 generics_0.1.3 ggridges_0.5.4
[73] evaluate_0.23 fastmap_1.1.1 ggdendro_0.1.23
[76] goftest_1.2-3 fitdistrplus_1.1-11 RANN_2.6.1
[79] pbapply_1.7-2 future_1.33.0 nlme_3.1-160
[82] mime_0.12 compiler_4.1.3 plotly_4.10.3
[85] png_0.1-8 spatstat.utils_3.0-4 stringi_1.8.3
[88] RSpectra_0.16-1 lattice_0.20-45 IRdisplay_1.1
[91] Matrix_1.6-4 ggsci_3.0.0 vctrs_0.6.5
[94] pillar_1.9.0 lifecycle_1.0.4 spatstat.geom_3.2-7
[97] lmtest_0.9-40 GlobalOptions_0.1.2 RcppAnnoy_0.0.21
[100] data.table_1.14.10 cowplot_1.1.1 irlba_2.3.5.1
[103] httpuv_1.6.13 patchwork_1.1.3 R6_2.5.1
[106] promises_1.2.1 KernSmooth_2.23-20 gridExtra_2.3
[109] IRanges_2.28.0 parallelly_1.36.0 codetools_0.2-18
[112] fastDummies_1.7.3 MASS_7.3-58.1 rjson_0.2.21
[115] withr_2.5.2 sctransform_0.4.1 S4Vectors_0.32.4
[118] parallel_4.1.3 hms_1.1.3 IRkernel_1.3.1
[121] Rtsne_0.17 pbdZMQ_0.3-8 spatstat.explore_3.2-5
[124] shiny_1.8.0 base64enc_0.1-3
​

junjunlab commented

Please given enough colors according the error infomation by using scale_color/fill_manual() function.

  • 👍1
CJ-Liu commented

@junjunlab I solved this error using the method you introduced. Thank you very much, and sorry that I did not notice this key prompt: “! Insufficient values in manual scale. 15 needed but only 9 provided.”

jjVolcano(diffData = pbmc.markers, log2FC.cutoff=0.25) +
scale_color_manual(values = cols) +
scale_fill_manual(values = cols)
note: cols is a vector that stores the color used

  • 👍1