Generate V23 figures

[sjspielman]

Closes #1674

This PR re-generates figure panels at V23. At this time, all panels are regenerated except snv-callers and tmb-compare panels for Figure S2 (because SQLite db's are still being regenerated). But, no diffs are expected in those figures either way. We can still circle back and re-generate them either in this PR or a subsequent one.

There is only one code change here, replacing plot title with Ependymoma, as related to #1652. https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/2c27261bcfe8fe9924b59c6112487a33c89806c6/figures/scripts/fig5_figS6-immune-deconv-panels.R#L259-L261

Again, I've made a spreadsheet cataloging all visible diffs, comparing these new PDFs to master: https://docs.google.com/spreadsheets/d/1Y3moe-xnLJ_o4Jhb-klcGeq-f6aPr28VzBUiWF_oD-8/edit?usp=sharing

Based on this, the following figures will need to be recompiled (I'm noting this in #1676 also). The relevant panels and/or figure aspect that necessitate the recompilation are in parentheses.

• Figure 1 (B)
• Figure 2 (all panels except maybe LGG, but let's say all panels)
• Figure 3 (A-D)
• Figure 4 (G and H)
• Figure 5 (legend for panel A, and maybe the heatmap in B but it really does seem ok to me)
• Figure S3 (A, C-D)
• Figure S5 (B-C; note there are no diffs in this PR, but these panels are different from V22 versions since we highlight TERTp now)
• Figure S6 (EPN panel title only; this involves only a quick text edit in Illustrator, no new panels)

[sjspielman]

• The extra figure<S>5.pdf files were removed in https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1677/commits/6a6ad53181a0f008732e487239da7ab930f2a9ff
• Embryonal oncoprint legend re-ordered to match plot in https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1677/commits/7a95473c8554c0d149cf63cc0f9d679741f79849

[sjspielman]

No changes in this PR run through CI, so we can merge before checks are complete.

[sjspielman]

Noting for #1652 that I have confirmed here that there are no more "Ependymal tumor" phrasings in figure panels.