V22 rerun figures for survival/tp53 telomerase

jharenza commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

Rerunning survival figures for v22.

What was your approach?

Reran:

Rscript --vanilla scripts/fig4-hgg-kaplan-meier.R
Rscript --vanilla scripts/fig4-hgg-subtype-forest-plot.R
Rscript --vanilla scripts/fig5-forest-plot.R
Rscript --vanilla scripts/fig4-tp53-telomerase-panels.R

What GitHub issue does your pull request address?

https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1368

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

Which areas should receive a particularly close look?

NA

Is there anything that you want to discuss further?

Reran all 4 scripts in full. Updated the x-axis code to show error bars for the tp53 telomerase FP.

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)?

What is your summary of the results?

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.

sjspielman commented 2 years ago

Thanks for opening this fresh PR! Thinking about it a bit more, I think it would be very appropriate to also use this PR to update the other figures in scripts/fig4-tp53-telomerase-panels.R. The tp53 rerun has been merged (#1461), and we are just waiting on checks to merge in #1475 (this is running through CI now quickly with a cache, so will get merged soon I suspect!).

Doing this will involve:

Re-running that script once both those PRs are merged
Updating groups here as needed: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/0c2b89ed5a8a3f9adb1963c4b54d924c9af0dfb1/figures/scripts/fig4-tp53-telomerase-panels.R#L251-L263
Making sure the seed set here still ensures that hypermutator points are all visible with the updated cancer groups. (when setting this originally I tried a bunch of seeds to make sure the hypermutator points aren't stacked on top of each other): https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/0c2b89ed5a8a3f9adb1963c4b54d924c9af0dfb1/figures/scripts/fig4-tp53-telomerase-panels.R#L126-L127
Checking in to make sure we've got all the right hypermutators

jharenza commented 2 years ago

Was thinking the same. Will do!

sjspielman commented 2 years ago

Noting this PR also closes #1417.

@jharenza can you also address #1373 for the forest plot here? I had missed that previously. The plot km_hgg_panel.pdf already has wording updated, but we need to fix forest_hgg_subtypes.pdf. Thanks!

jharenza commented 2 years ago

@jharenza can you also address #1373 for the forest plot here? I had missed that previously. The plot km_hgg_panel.pdf already has wording updated, but we need to fix forest_hgg_subtypes.pdf. Thanks!

Sure! Just pushed the other updates mentioned above. Stand by :)

jharenza commented 2 years ago

@sjspielman this should be ready now. Note: I used the same cancer groups as in interaction plots (minus "Other" ) to 1) be consistent with something else and 2) to include the "other embryonal tumor", which contains the new NBL metastasis hypermutator. Seed still works fine.

jharenza commented 2 years ago

ok @sjspielman - updated seed and reran. I was looking at mainly whether they were visible so was thinking some overlap was ok.. I see what you mean now!

sjspielman commented 2 years ago

This code does not run through CI, so merging before checks complete.

AlexsLemonade / OpenPBTA-analysis