Using mapping histology groups for plotting -- Part 2 implemention (PR 2 of 4)

[cansavvy]

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR addresses Step 3 and part Step 4 discussed in #897 and #898. This PR is updating modules that should now be using the palettes/histology_label_color_table.tsv table that is created by the notebook added in #899

What was your approach?

This PR is 2 of a few PRs where I am updating things in response to the table added in #898

Here's what's accomplished in this PR and what files have changes that need review (the rest are updated plots):

• cnv-chrom-plot/cn_status_heatmap.Rmd now uses the histology groupings and hex code colors from histology_label_color_table.tsv
• mutational-signatures/known_signature.Rmd now uses the histology groupings and hex code colors from histology_label_color_table.tsv
• I also needed to update the custom functions in mutational-signatures/util so that they used display_group instead of short_histology for the plotting.

I deleted the old plots, re-ran both of the notebooks mentioned above, and now am pushing the updated plots and results. That's where the crazy number of files changed comes from, a lot of plot updates.

*Note that the palettes/histology_color_palette.tsv file itself is not deleted yet, I will do this in the last PR of this series so the other modules that use this file don't break in CI yet.

What GitHub issue does your pull request address?

Makes more progress toward addressing #898

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

Which areas should receive a particularly close look?

• How do we feel about how the updated chromosomal-instability heatmap plots look? (see zip file below if you don't want to check out the branch)
• Is the figures/README updated appropriately and with enough detail?

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

Yes. Here's updated cn status heatmap from cnv-chrom-plot:

And here's some of the updated plots from the known signature analysis in mutational-signatures (I did not included the signature_grouped_barplots folder of plots; it was too big.

Results

What is your summary of the results?

Plots are different and now use the display_group histology labels instead of short_histology.

Note that cnv-chrom-plot does not use the histology color palette, but it does still use short_histology for its plots -- *I have not updated this notebook here, we should discuss if we should update that in another PR. *

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile. -- no new packages are needed.
• This analysis has been added to continuous integration.

Documentation Checklist

I checked the respective READMEs for these analyses and they did not require any updates for these changes.

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

[jashapiro]

Looks good to me. Just one comment because I don't trust the machines.

[jashapiro]

I'm a little worried about separate unique() calls preserving order... I think it should work fine, but it seems somehow dangerous to me. So I present an alternative below.

Suggested change

	histologies_color_key_filtered <- unique(histologies$hex_codes)
	names(histologies_color_key_filtered) <- unique(histologies$display_group)
	histologies_color_key_filtered <- histologies %>%
	dplyr::select(display_group, hex_codes) %>%
	dplyr::distinct() %>%
	dplyr::pull(hex_codes, name = display_group)

[cansavvy]

Yes. I like this better.

[cansavvy]

Turns out the name argument for pull is not in our version of dplyr for our docker image, so I can't use the last part, but I will add a distinct to this part but in my subsequent PR of this series.