V22 rerun sample distribution figure

[jharenza]

❗ stacked on #1401

Purpose/implementation Section

What scientific question is your analysis addressing?

Update code to rerun the sample distribution figure using cancer_group_display

What was your approach?

• Added an earlier merge of the palette into the histologies file for counting by cancer group display.
• Updated relevant parts of code to use cancer group display

What GitHub issue does your pull request address?

1368

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

The assay legend is not printing, and I am not sure why. Double check the code updates!

Is there anything that you want to discuss further?

See above.

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

sample distribution figures

What is your summary of the results?

The updates (minus assay panel) look to have been implemented.

Reproducibility Checklist

• [x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• [x] This analysis has been added to continuous integration.

Documentation Checklist

• [x] This analysis module has a README and it is up to date.
• [x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [x] The analytical code is documented and contains comments.

[jharenza]

@sjspielman reran with the latest from #1401 - had to update a join, but looks good. also removed the code (and folder+plots) for the plots not in use.

[jharenza]

@jaclyn-taroni and @sjspielman this one is ready for re-review

[jharenza]

We can remove this line from fig1-sample-distribution.R at this point -

library(ggpattern)

In fact, after greping the whole repo, it seems this script was the only place ggpattern was needed. In theory we can remove this installation from the Dockerfile as well, which may also help in the fight against rate limits (#1469). I don't think I'd do that in this PR, however - if we want to do that, we should open separately.

Otherwise it looks good to me!

updated