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 (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.