Revision: Updates to sample distribution analysis module - Githubissues

AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project

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Revision: Updates to sample distribution analysis module #1642

Closed jharenza closed 1 year ago

jharenza commented 1 year ago

Purpose/implementation Section

What was your approach?

Add patient N per cohort calculation in 04-ns-for-manuscript.Rmd
Remove script 02-multilayer-plots.R from this module, update README. It appears treemapify was removed from the docker image as this part of the analysis has been deprecated, so I have updated the bash script and README to reflect this and enable a rerun.

https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/aa54a954cb2b0c5c5342c0c7284275e35a8f5505/Dockerfile#L206-L207

What GitHub issue does your pull request address?

NA, revision request - Reviewer 1, point 5

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)?

Notebook

What is your summary of the results?

Number of CBTN patients: 911 Number of PNOC patients: 32 (Total = 943)

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.