This PR updates code for Figure S3 as well as updates its compiled PDF and PNG. The specific changes are as follows:
One goal for S3 is to include the new tumor purity violin plot as panel A, meaning other panels need to be bumped a letter. The code for these figures was pretty prescriptive about the panel names, so I went ahead and updated to be less prescriptive about the panels. This resulted in changed file names and minor code changes:
figS3-panels-BCD.R is now called figures/scripts/figS3-panels-cn-chromothripsis.R, and it exports slightly differently named (but otherwise unchanged) PDFs
The change to the script name is also updated in figures/scripts/README.md
To facilitate compilation, I did some minor sizing tweaks for the tumor purity violin plot in analyses/tumor-purity-exploration/01_explore-tumor-purity.Rmd, and re-generated the notebook that generates/exports it.
I updated figures/generate-figures.sh to run the script with this new name, and to copy the tumor purity panel over into figures/pdfs/.
Closes #1675 Related to #1676
This PR updates code for Figure S3 as well as updates its compiled PDF and PNG. The specific changes are as follows:
figS3-panels-BCD.Ris now calledfigures/scripts/figS3-panels-cn-chromothripsis.R, and it exports slightly differently named (but otherwise unchanged) PDFsfigures/scripts/README.mdanalyses/tumor-purity-exploration/01_explore-tumor-purity.Rmd, and re-generated the notebook that generates/exports it.figures/generate-figures.shto run the script with this new name, and to copy the tumor purity panel over intofigures/pdfs/.