krassowski
Set default color of dots in the matrix plot
Is your feature request related to a problem? Please describe. Set default color of dots in the matrix plot.
Describe the solution you'd like An argument to the upset() function that would allow me to set the default colors for the dots in the matrix plot (ideally, for the default color values for the whole plot).
Currently these default values are hard coded in upset.R line 1092.
matrix_default_colors = list(`TRUE` = "black", `FALSE` = "grey85")
Describe alternatives you've considered
Currently, since upset() depends on non-exported functions, I can only think of cloning the GitHub repository, altering the function and reinstalling the modified library.
Context (required)
ComplexUpset version: 1.4.0
R version details
$platform
[1] "x86_64-w64-mingw32"
$arch
[1] "x86_64"
$os
[1] "mingw32"
$crt
[1] "ucrt"
$system
[1] "x86_64, mingw32"
$status
[1] ""
$major
[1] "4"
$minor
[1] "3.1"
$year
[1] "2023"
$month
[1] "06"
$day
[1] "16"
$`svn rev`
[1] "84548"
$language
[1] "R"
$version.string
[1] "R version 4.3.1 (2023-06-16 ucrt)"
$nickname
[1] "Beagle Scouts"
R session information
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.14.8 patchwork_1.1.3 ggpubr_0.6.0 ggplot2_3.4.3 ComplexUpset_1.3.3 tibble_3.2.1 reshape2_1.4.4 purrr_1.0.2
[9] tidyselect_1.2.0 tidyr_1.3.0 dplyr_1.1.3 magrittr_2.0.3 here_1.0.1
loaded via a namespace (and not attached):
[1] viridisLite_0.4.2 farver_2.1.1 viridis_0.6.4 Biostrings_2.68.1 bitops_1.0-7 fastmap_1.1.1
[7] lazyeval_0.2.2 RCurl_1.98-1.12 digest_0.6.33 lifecycle_1.0.3 tidytree_0.4.5 compiler_4.3.1
[13] rlang_1.1.1 tools_4.3.1 utf8_1.2.3 yaml_2.3.7 knitr_1.43 ggsignif_0.6.4
[19] labeling_0.4.3 plyr_1.8.8 RColorBrewer_1.1-3 aplot_0.2.0 abind_1.4-5 withr_2.5.0
[25] BiocGenerics_0.46.0 grid_4.3.1 stats4_4.3.1 fansi_1.0.4 colorspace_2.1-0 scales_1.2.1
[31] cli_3.6.1 rmarkdown_2.24 crayon_1.5.2 treeio_1.24.3 generics_0.1.3 rstudioapi_0.15.0
[37] ggtree_3.8.2 ape_5.7-1 cachem_1.0.8 stringr_1.5.0 zlibbioc_1.46.0 parallel_4.3.1
[43] ggplotify_0.1.2 XVector_0.40.0 yulab.utils_0.0.9 vctrs_0.6.3 jsonlite_1.8.7 carData_3.0-5
[49] car_3.1-2 gridGraphics_0.5-1 IRanges_2.34.1 S4Vectors_0.38.1 rstatix_0.7.2 wesanderson_0.3.6
[55] ggdendroplot_0.1.0 glue_1.6.2 stringi_1.7.12 gtable_0.3.4 GenomeInfoDb_1.36.3 munsell_0.5.0
[61] pillar_1.9.0 htmltools_0.5.6 GenomeInfoDbData_1.2.10 R6_2.5.1 rprojroot_2.0.3 evaluate_0.21
[67] lattice_0.21-8 backports_1.4.1 memoise_2.0.1 broom_1.0.5 ggfun_0.1.2 Rcpp_1.0.11
[73] gridExtra_2.3 nlme_3.1-163 xfun_0.40 pkgconfig_2.0.3
See https://krassowski.github.io/complex-upset/articles/Examples_R.html#adjusting-the-intersection-matrix. Also, #181 it will also allow to customise outline.
There is no such a barrier in R as non-exported functions, you can just use triple colon like ComplexUpset:::function_name
