N per cancer_group oncoprint

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Add Ns per cancer_group used in oncoprint

What was your approach?

I updated the script that 01-map-to-sample-id.R to generate the Ns because the script filters the input data used in oncoprint generation.

What GitHub issue does your pull request address?

1182

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

Which areas should receive a particularly close look?

• titleText in the oncoplot function seems to be invalid now? We did update maftools recently
• There is a step to remove ambiguous sample_id where there are more than two Tumor_Biospecimen_ID from the same experimental_strategy is present. I filtered the histology with the same filtering to be consistent with what the denominator would be for frequencies reported in oncoprint. Please let me know if that is not required here. Thanks!

Is there anything that you want to discuss further?

NA

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)?

tables

What is your summary of the results?

Added analyses/oncoprint-landscape/data/primary-plus_n_per_cancer_group.tsv with Ns per cancer_group

Reproducibility Checklist

• [x] 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

• [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.