Updated analysis: update oncoprint

[jharenza]

What analysis module should be updated and why?

oncoprint

What changes need to be made? Please provide enough detail for another participant to make the update.

1. Update color level for c-circle NEG vs NA:

https://github.com/d3b-center/Cole-telomere-analysis/blob/f655ac13e4d383de4cba18dd3365b14b767b0d04/analyses/oncoplot/plot_oncoplot.R#L45-L46

Let's recode NA to Not done so it shows up in the legend and pick a darker grey

2. Add an annotation track for "Mutation status" and pick some pretty colors? 😅 :

   mutate(
   `Mutation status` = case_when(
     tmb < 10 ~ "Normal",
     tmb >= 10 & tmb < 100 ~ "Hypermutant",
     tmb >= 100 ~ "Ultra-hypermutant")
   )

3. TBD later (new ticket) - annotate VUS/driver using OncoKB, possibly?

What input data should be used? Which data were used in the version being updated?

same as before, with updated excel sheet patient subset

When do you expect the revised analysis will be completed?

by april 15

Who will complete the updated analysis?

@runjin326

[jharenza]

completed in #21