add Table 2

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

Add Table 2 for manuscript

What was your approach?

• Created Table 2, manually add therapy and updated cancer predispositions where necessary
• also updated 08-explore_hypermutators.Rmd to add composition since one of the samples is a cell line and we did not use that for the final table

What GitHub issue does your pull request address?

1318

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?

no

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

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

Documentation Checklist

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

[jharenza]

@sjspielman changes are in! I updated the heatmap here, and realized that the matrix and annotations on the map with the new samples were not in the same order, so fixed that as well. The new results are in https://github.com/AlexsLemonade/OpenPBTA-manuscript/pull/243

[sjspielman]

This is failing CI I think because of a bug that we missed in a previous PR - the run_mutational_signatures.sh script doesn't pass in the CI param. I'm adding a quick commit to hopefully fix this.

[jharenza]

Note @sjspielman - I kept the BS_IDs in the plot for purposes of being able to write, so we can either remove this in the module or in illustrator. Wasn't sure if you wanted this for any manuscript review.

[jharenza]

Not technically part of the code changes here, but I think we should also relabel the x-axis of the heatmap to "RefSig Mutational Signature Weights" or "RefSig Mutational Signature Exposures"

updated

[sjspielman]

I kept the BS_IDs in the plot for purposes of being able to write, so we can either remove this in the module or in illustrator.

Totally fine by me.

[jharenza]

This looks ready to go but needs one important change! The heatmap panel and legend should be copied over to figures/pdfs/fig4/panels/ manually.

See here.

yes, good catch! done!

[sjspielman]

I see some conflicts have popped up - I'm going to go in now and fix manually and then this should be ready.

[jharenza]

some weird things happened from conflict resolution, but this should be all set now @sjspielman

[sjspielman]

Went through and re-ran all notebooks to confirm everything is cleaned up and it looks good. Thanks for catching those conflict issues!

This has passed CI and no commits since will affect CI, so this can be merged in before checks are completed.