Update plot_num_subclones_box.R

[philippaSteinberg]

Change orientation of x and y and increase sizes of fonts

Description

Changed the orientation of box plots (patients x n_subclones) and changed label font size.

Pipeline Run Results

Run script to generate one plot

module load R

Rscript ./plot_num_subclones_box.R \
-f /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-phylowgs/output/2023-04-23_num_subclones_mutect2_battenberg_pyloWGS_sr.tsv \
-p Mutect2-Battenberg-PhyloWGS \
-m sr \
-o /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/plots/boxplot/

Checklist

• [x] This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
  Disclosing PHI is a major problem[^1] - Even a small leak can be costly[^2].

• [x] This PR does NOT contain germline genetic data[^3], RNA-Seq, DNA methylation, microbiome or other molecular data[^4].

[^1]: UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records [^2]: The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. [^3]: Genetic information is considered PHI. Forensic assays can identify patients with as few as 21 SNPs [^4]: RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity.

• [x] This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

• [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.

[philippaSteinberg]

@lydiayliu sent u an email regarding this !

[lydiayliu]

I believe this could be updated to the finalized script? @philippaSteinberg