Updated sample distribution panel for figure 1

[sjspielman]

Purpose/implementation Section

What was your approach?

We need a new approach for visualizing the sample counts and their respective broad histologies, cancer groups, and tumor descriptors. Previously a new plot was made in https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1201, but the labeling will prohibit the figure from fitting into a panel in main text Figure 1.

This new approach "cleans up" the previous version for improved legibility in the main text. Notably, this is partly achieved by using abbreviations for the cancer groups where appropriate, and the abbreviations have also been integrated into mapping-histology-labels.Rmd, which in turn added a new column cancer_group_abbreviations to broad_histology_cancer_group_palette.tsv. Those abbreviations are now also shown in the cancer group legend stub within mapping-histology-labels.Rmd.

What GitHub issue does your pull request address?

1175

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

Which areas should receive a particularly close look?

• Are we ok fully integrating abbreviations into the notebook and palette TSV? My sense was this is preferred so that we can track the abbreviations as part of the legend for cancer groups. The hope is this change DOES NOT break the build, and we will find out soon here.
• Any figure aesthetics we want to discuss

Is there anything that you want to discuss further?

N/A

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

Yes

Results

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

• Updated palette notebook and histology palette file to contain abbreviations
• Figure 1 sample distribution panel

What is your summary of the results?

N/A

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.

[sjspielman]

Wait a second.. I accepted the commit with the changed = to <-, but was that right? I think the = was correct. Line 185 is not creating a new variable, but a column in a df.

[jaclyn-taroni]

Oops, diffs are hard!

[sjspielman]

Here's a figure with angled labels. It looks funky for the facets with only 1 subgroup, but cleaner for the multiple subgroups eg fitting Schwannoma label. I'm pretty neutral on angled or not angled for this one. tumor_descriptor_proportion_panel.pdf

[jaclyn-taroni]

My slight preference is angled.

[sjspielman]

Closes #1175.