gmt music plot mutation-relation

NAME

gmt music plot mutation-relation - Makes plots for results from the mutation-relation tool

VERSION

This document describes gmt music plot mutation-relation version 0.04 (2018-07-05 at 09:17:13)

SYNOPSIS

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

REQUIRED ARGUMENTS

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

OPTIONAL ARGUMENTS

skip-zero-mut-samples Boolean

Don't plot samples that have no mutations on any gene being plotted

Default value 'true' if not specified

noskip-zero-mut-samples Boolean

Make skip-zero-mut-samples 'false'

genes-to-plot String

Comma-separated list of genes to plot (example: DNMT3A,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

noplot-genes-in-order-listed Boolean

Make plot-genes-in-order-listed 'false'

DESCRIPTION

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