Plot seed variability

[philsteinberg]

Description

Script for scatterplot comparing the number of subclones observed with the mode number of subclones observed across all 10 seeds.

Closes #99

Checklist

• [x] This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
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• [x] I have read the code review guidelines and the code review best practice on GitHub check-list.
• [x] I have set up or verified the main branch protection rule following the github standards before opening this pull request.
• [x] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
• [x] I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Analysis Results

• Case 1
  • script:
    /hot/users/psteinberg/git/project-SRC-RandomSeed/src/output-analysis/plotting/subclone_relative_seed_variability.R
  • command:

    Rscript ./subclone_relative_seed_variability.R -f /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-pyclone-vi/output/2023-04-02_num_subclones_strelka2_battenberg_pyclone-vi_sr.tsv -p Strelka2-Battenberg-PyClone-VI -m sr -o /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/plots/stripplot/ 

  • output:
    /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/plots/stripplot/2023-04-17_proj-seed_Strelka2-Battenberg-PyClone-VI_sr_relative_seed_var.pdf

[philsteinberg]

Ran all of the TEST files from the script in R studio. Not sure why running the above command in VSCode does not work. I loaded R and submitted the example command. Do I need to load other modules or set up an environment to run Rscripts from the command line? I am not sure why module load argparse does not work.

Error in library(argparse) : there is no package called ‘argparse’

[lydiayliu]

mean number of subclones

Do you mean mode?

Ran all of the TEST files from the script in R studio. Not sure why running the above command in VSCode does not work. I loaded R and submitted the example command. Do I need to load other modules or set up an environment to run Rscripts from the command line? I am not sure why module load argparse does not work.

argparse is probably not installed for R on the cluster. Doing module load doesn't load additional R packagaes unforatunately. You should be able to do install.packages('argparse') in interactive R on the cluster to install it.

[philsteinberg]

Do you mean mode?

Yes, sorry, corrected.

argparse is probably not installed for R on the cluster. Doing module load doesn't load additional R packagaes unforatunately. You should be able to do install.packages('argparse') in interactive R on the cluster to install it.

Thanks, it works.