Figure Panel: Oncoprint Landscape

[cbethell]

As depicted in the sketch of the landscape of genomic alterations figure in the manuscript, the oncoprint figure found in analyses/oncoprint-landscape/plots should be updated and made publication ready. (Related to: #571)

Updating/making this figure publication ready will consist of:

• Incorporating the list of genes in the gene_disease_top50.tsv generated and saved in the results directory of analyses/interaction-plots to filter to genes with mutations of interest interest that should be represented on the oncoprint
• Incorporating a list of CNA genes that should be represented on the oncoprint (after PR Add cytoband to copy number files using bedtools intersect #617 is merged, lists of the "most focal unit" generated (WIP PR WIP: Resolving "gene-level" copy number alterations with broader alterations #485) and recurrent copy number alterations determined (Updated analysis: Recurrently Altered Genes CNV and SV data #488)
• Updating the script to use the most recent consensus files where applicable (consensus CN files)
• Updating the script to use the color palettes generated in PR Updated analysis: Unified color palette for plots #510
• Creating a separate script for putting the oncoprint in a figure panel

I plan to work on this sometime this sprint.

[jaclyn-taroni]

I'm going to call this closed by #666 and subsumed by #706.