Figure S7: Add new panels A and C

[sjspielman]

Part of #1691

Closes #1694 Closes #1696

This PR adds two panels for Figure S7 and updates some of the existing scaffoldings, as follows:

1. Add new a panel A with the script figures/scripts/figS7-seqcenter-barplot.R.
   • This script exports the panel figures/pdfs/supp/figs7/panels/RNA_library_barplot.pdf for use in the supplementary figure.
   • This script was also recorded in figures/scripts/README.md.
2. Update the notebook analyses/transcriptomic-dimension-reduction/04-explore-sequencing-center-effects.Rmd to export the relevant plot needed for panel C.
   • Plot is exported to analyses/transcriptomic-dimension-reduction/plots/umap_cancer-group_sequencing-center.pdf.
   • This also involved some minor code tweaks for pub-ready plot styling. The notebook was rerun, and the module README.md was updated to note this exported plot.
3. figures/generate-figures.sh was updated as follows:
   • Run the new figures/scripts/figS7-seqcenter-barplot.R script
   • Copy the UMAP panel into figures/pdfs/supp/figS7/panels.
   • Update comments to indicate new panel order

[sjspielman]

Noting I'm requesting review from @jaclyn-taroni which can alternatively be interpreted as requesting @jaclyn-taroni to request someone else! :)

[sjspielman]

@jashapiro ready for another look!

• In https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1698/commits/92c0d3a609fff4fea45e196cc6291b9a46189a26 I added some comments to clarify some of the code order in generate-figures.sh
• In https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1698/commits/394148d476518f794fe34ce18b855785521f9a35 I bumped the output PDF size
  • PDF here: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/394148d476518f794fe34ce18b855785521f9a35/figures/pdfs/supp/figs7/panels/RNA_library_barplot.pdf