michaelcurry1123

The package `colorblindcheck` will help. here is a useful blog: https://cran.r-project.org/web/packages/colorblindcheck/vignettes/intro-to-colorblindcheck.html ``` library(gnomeR) library(colorblindcheck) lapply(gnomer_palettes, palette_check) ``` > $pancan > name n tolerance ncp ndcp min_dist mean_dist max_dist > 1...

ok so there is a way to find the colorblind pairs and we might be able to turn it into a function. here is a very rough sketch of what...

function for this: ``` noncolorblindfriendlypairs

colorspace package might help

@karissawhiting I never opened a branch or pr for this just put the functions in an issue!

``` mut2 % group_by(sampleId,hugoGeneSymbol) %>% filter(row_number()==1) %>% ungroup() %>% tidyr::pivot_wider( id_cols = "sampleId", names_from = "hugoGeneSymbol", values_from = "mutationType", values_fill = "None") ``` This is the basis of the code...

can they have two of the same type of mutations (eg. two fusions on the same gene) or would it be a mutation, fusion or cna? @karissawhiting

ok no problem did that!

``` mut2 % group_by(sampleId,hugoGeneSymbol,mutationType) %>% filter(row_number()==1) %>% ungroup() %>% group_by(sampleId, hugoGeneSymbol) %>% summarise(alteration = paste(mutationType, collapse = ",")) %>% ungroup() %>% mutate(alteration = ifelse(grepl(",", alteration), "Multiple Mutations",alteration )) cna2 %...

@karissawhiting I think this code gets us some of the way there, it is wide, addresses multiple fusions and cna. will have to look into the other stuff though also...