genome music plot mutation-relation
NAME
genome music plot mutation-relation - Makes plots for results from the mutation-relation tool
VERSION
This document describes genome music plot mutation-relation version 0.0401 (2014-02-13 at 08:01:08)
SYNOPSIS
genome 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.