Compiled figure S7

[sjspielman]

Closes #1665

This PR adds a compiled figure S7, which shows results generated at a tumor purity threshold. This figure may or may not be used in the MS (given supplementary figure journal restrictions), but we have it in case as well as to use during response to reviews.

In addition to the PNG and PDF files, there are some minor code changes:

• I had to add useDingbats=FALSE to ggsave() statements in analyses/tp53_nf1_score/10-tp53-tumor-purity-threshold.Rmd for the two tp53 violin plot panels (tp53-score-status_tumor-purity-threshold.pdf and tp53-fpkm-status_tumor-purity-threshold.pdf)
  • I re-ran this notebook to re-generate those plots (heads up, that rendered HTML lives elsewhere: analyses/tp53_nf1_score/results/tumor-purity-threshold/10-tp53-tumor-purity-threshold.nb.html)
  • I copied over the updated figure panels to figures/pdfs/supp/figs7/panels/
• I updated comments in figures/generate-figures.sh and the table in figures/scripts/README.md to indicate which panels the plots ended up as

[sjspielman]

Note to self, this does need to run through CI before merge since tp53_nf1_score code changed.

[sjspielman]

@jashapiro this is ready for another look now! I recompiled it, and then realized when the plots were different that the code was missing a seed, so another rinse/repeat there.