V23 manuscript run

[sjspielman]

I am opening this PR as a Draft as it is, well, a lot...and perhaps it needs to be split up.

This PR represents a local Big Run - RUN_LOCAL=1 bash scripts/run-manuscript-analyses.sh, and there are rather a lot of diffs. I have tried to catalog how I handled everything in this spreadsheet: https://docs.google.com/spreadsheets/d/1xRGlPYzfMcGnLBIMGTJuHJ5LyCyOSuIOKcp_GyGKMnU/edit?usp=sharing Within this spreadsheet, I indicate for each file that has a diff whether I indeed committed it or just checked it out (so it won't appear in this PR as a diff!) because it was already reasonably up-to-date. I made the decision to generally commit binary files even if there were no apparent diffs due to file metadata which will likely have changed to better reflect that the file was generated with V23. I've highlighted a couple rows in the spreadsheet that I think are worth definitely checking.

There is also one easy thing to review here! I updated to V23 in figures/generate-figures.sh. The rest is less easy but I hope the spreadsheet will help, and/or a new strategy for merging all this in.

From this endeavor, I identified that at least these figure panels will need to be updated for resubmission, and associated figures recompiled -

• Figure 3
  • interaction panels A-B
  • chromothripsis panels C-D)
• Fig 2 - all oncoprints
• Fig S5A-D oncoprints
  • Note that S5 compilatio needs to be updated to say "Ependymoma" as well anyways (#1652)
• Survival plots
  • HGG KM curve (4H)
  • likely some of the survival forest plots (potentially 4F-H and 5D)

[jaclyn-taroni]

I went through the spreadsheet and took a look at the highlighted rows. I believe the changes in chromothripsis and interaction-plots are due to the changes in the independent specimen files. That is also likely true in the recurrently fused fusions files, as the stranded independent RNA-seq specimens file changed between v22 and v23. I have identified what I think is the cause of the addition of the RN7SL2--IGF2 lines in analyses/fusion_filtering/results/pbta-fusion-putative-oncogenic.tsv here: https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1672#discussion_r1111323796

All that to say – I don't believe anything here is concerning at this point.

[sjspielman]

Opening this up for "formal review" since things look mostly accounted for. Spelunk away!

[sjspielman]

There are no code changes here that are part of CI, so this can be merged before checks.