Create minimal main display item palette (AlexsLemonade#1176) (AlexsL…

…emonade#1193)

* Initial pass at histology palette overhaul

* Add display columns for legends

* Remove histology label palette NB from CI

* Add broad histology order

* Add oncoprint_include

* Add oncoprint grouping info to palette df

* Make cancer_group other darker; rerun

* Missed the instance where I recode based on other hex code

* Change up approach to oncoprint

* Tweak the cancer group palette

* Apply suggestions from code review

Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

* Also display other hex codes with legend()

Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

.circleci/config.yml

@@ -20,10 +20,6 @@ jobs:
           name: Check python packages
           command: ./scripts/run_in_ci.sh bash scripts/check-python.sh
 
-      - run:
-          name: High level histology grouping for plot labels
-          command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('figures/mapping-histology-labels.Rmd', clean = TRUE)"
-
       - run:
           name: Sample Distribution Analyses
           command: ./scripts/run_in_ci.sh bash "analyses/sample-distribution-analysis/run-sample-distribution.sh"