maf_matrix

Create matrix plots from TCGA MAF files

Simply provide a path to a maf file and a list of genes, and the script can either:

1. save the matrix figure (to an optional path). (The "-a" flag shows all patients.), or
2. look up the amino acid changes from Broad's Oncotator and print out text that can be used in the CBioPortal oncoprinter tool.

Example matrix image:

Example oncoprinter image:

Using the executable

plot_maf_matrix [-h] -i MAF_PATH [-t | -o OUT_PATH] [-a]
                       [-g GENES [GENES ...]]

optional arguments:
  -h, --help            show this help message and exit
  -i MAF_PATH, --maf_path MAF_PATH
                        Path to maf file.
  -t, --oncoprinter
  -o OUT_PATH, --out_path OUT_PATH
                        Output figure path including extension.
  -a, --all_patients    Show all patients in matrix plot.
  -g GENES [GENES ...], --genes GENES [GENES ...]
                        Gene hugo symbols, case sensitive.

e.g. for first matrix plot shown above:

plot_maf_matrix -i hgsc.bcm.edu_CHOL.IlluminaGA_DNASeq.1.somatic.maf -o test_matrix.pdf -g MUC4 TP53 KRAS BRAF NF1

Using the python module

https://dl.dropboxusercontent.com/u/5141228/matrix_demo.html

Installation

• unzip the archive and run

python setup.py install

License

Copyright (C) 2015 Stephen Gaffney

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.