Splitting up #921: GSEA module changes

[cansavvy]

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR is a split off of #921 where I am updating the transcriptomic overview plot in response to the histology color palette table added in #898.

This module focuses on updating gene-set-enrichment analysis.

This PR updates gene-set-enrichment-analysis module to use the display group and hex codes of the palettes/histology_label_color_table.tsv table that is created by the notebook added in #899

What was your approach?

This PR updates one of the three modules that are ultimately used in the transcriptomic-overview plot that is ultimately updated in #921.

gene-set-enrichment analysis updates:

• gene-set-enrichment-analysis/02-model-gsea.Rmd was updated from using short_histology for the gsea model to using display_group
• Related to gene-set-enrichment-analysis, the source script: analyses/gene-set-enrichment-analysis/util/hallmark_models.R needed a dplyr:: in one spot because it wouldn't run.
• There was also a slight detour error that need to be fixed (but ended up being a quick fix) in 01-conduct-gsea.R See Updated analysis: GSEA throws error with stranded collapse-rnaseq v18 data #926
• After these changes I re-ran run-gsea.sh

*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 (#927) 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
Closes #926

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

• Is there anything I missed?

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

Yes

Results

Results files that were reporting short_histology are now replaced with files that report display_group.

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.

[cbethell]

Based on the upstream changes made in #899, the updates to the notebooks/scripts and the resulting files in this PR make sense!

I double checked this module and it does not seem that you missed anything and I was able to rerun the module's bash script and reproduce your results. That said, LGTM!