Set default color of dots in the matrix plot

[thiagomaf]

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        

[krassowski]

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