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gmt-music-plot-mutation-relationp - Online in the Cloud

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This is the command gmt-music-plot-mutation-relationp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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