V22 rerun survival figures

[jharenza]

❗ stacked on #1464

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR updates all associated survival figures for Figures 4 and 5.

What was your approach?

I reran the following scripts:

Rscript --vanilla scripts/fig4-hgg-kaplan-meier.R
Rscript --vanilla scripts/fig4-hgg-subtype-forest-plot.R
Rscript --vanilla scripts/fig5-forest-plot.R

and only ran the forest plot for scripts/fig4-tp53-telomerase-panels.R

What GitHub issue does your pull request address?

1368

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

Which areas should receive a particularly close look?

I added the couple of scripts into the generate-figures.sh even though I know you have the script updated in PR, just in case those are missing currently (didn't check your PR!).</s disregard now that the PR is merged

I had to update the x-axis for the tp53 telomerase forest plot in order to get LGG group to show up, and then further updated it to be able to get the full confidence intervals to show up. The axis went back to scientific notation, but don't think this is a big deal. Let me know what you think.

Is there anything that you want to discuss further?

See above

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

Yes

Results

What types of results are included (e.g., table, figure)?

Updated KM plot and 3 forest plots

What is your summary of the results?

NA

Reproducibility Checklist

• [x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• [x] This analysis has been added to continuous integration.

Documentation Checklist

• [x] This analysis module has a README and it is up to date.
• [x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [x] The analytical code is documented and contains comments.

[jharenza]

@sjspielman this is ready for review. ran with your latest updates in #1464

[sjspielman]

We're going to need to take a step back here... Because this was "semi-stacked" on #1464, there are quite a few diffs in the survival module itself. But, since the module itself doesn't produce any manuscript figures, this PR should only be re-running, and updating where needed, these four scripts - fig4-hgg-subtype-forest-plot.R, fig4-tp53-telomerase-panels.R, fig4-hgg-kaplan-meier.R, and fig5-forest-plot.R. I'd therefore close this PR and open a new one which only runs (and updates where needed) the scripts of interest.

Also, we need to be cognizant that fig4-tp53-telomerase-panels.R is making other figures that are exported but will need to be updated separately, which I see is part of the list in #1368. But, I don't see that that script was actually re-run here since I would have expected more byte-size PDF diffs (?). Even though we only want to capture the forest plot section for this PR, make sure the full scripts are run in case of bugs for the new PR.

[jharenza]

Also, we need to be cognizant that fig4-tp53-telomerase-panels.R is making other figures that are exported but will need to be updated separately, which I see is part of the list in https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1368. But, I don't see that that script was actually re-run here since I would have expected more byte-size PDF diffs (?). Even though we only want to capture the forest plot section for this PR, make sure the full scripts are run in case of bugs for the new PR.

Yeah, noted above, I only ran the FP part of the code, but will open a new PR and run full scripts.