gnomeR

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Colorblind color palette

8

- first check if our current ones are color blind friendly- @karissawhiting will find the tool that can help with this from mskRvis - If not, add a color blind...

karissawhiting

hfuchs5

**What changes are proposed in this pull request?** Updated ggcorr plotting functions to include argument to select genes to plot **If there is an GitHub issue associated with this pull...

toumban1

Add an example to vignette and/or docs that changes color palette of the ggcor or ggcomut plot

2

Could just be me, but maybe having an example of how to change the color palette for one of these plots would be helpful?

hfuchs5

Currently `subset_by_frequency()` will subset and only return alteration columns in your gene binary with > x% prevalence. Sometimes it's useful to calculate these frequency/inclusion cutoffs by keeping genes or alterations...

karissawhiting

**What changes are proposed in this pull request?** **To-do's before merging** - [ ] Bring in any comments over from other PR and close that PR (https://github.com/MSKCC-Epi-Bio/gnomeR/pull/307). All code changes...

karissawhiting

unit testing for tbl_genomic(..., wide = T) needed

1

hfuchs5

Add annotation of point mutations in create gene binary pipeline

3

We can require this as a preprocessing step, or add an arg in `create_gene_binary()`. We will think on it more and maybe ask Caroline and Alli for preference. Maybe we...

karissawhiting

**What changes are proposed in this pull request?** Added var_class attribute option to `create_gene_binary()` which retains a long form of the mutation/fusion/cna files with variant_classification values. Haven't made official tests...

hfuchs5

#335 #263

hfuchs5