genome-music-plot-mutation-relation (1p)

This document describes genome music plot mutation-relation version 0.04 (2013-05-14 at 16:03:04)

genome music plot mutation-relation --input-matrix=? --output-pdf=? [--skip-zero-mut-samples] [--genes-to-plot=?] [--plot-genes-in-order-listed]

input-matrix String

A gene/sample matrix generated by the mutation-relation tool

output-pdf String

An output pdf file to draw the plot to

skip-zero-mut-samples Boolean

Don't plot samples that have no mutations on any gene being plotted Default value 'true' if not specified

genes-to-plot String

Comma-separated list of genes to plot (example: \s-1DNMT3A\s0,NPM1)

plot-genes-in-order-listed Boolean

Plot the genes in the order that they're listed. Default is to plot them in descending order by number of mutations Default value 'false' (--noplot-genes-in-order-listed) if not specified

Given a matrix generated using \*(L"music mutation-relation --mutation-matrix-file\*(R", this tool will generate a plot that highlights mutual exclusivity or concurrence between the mutation status of a predefined set of genes.