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PROGRAM:

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 (2016-01-01 at
23:10:19)

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.

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