#gd3

A library of genomics visualizations.

1. Requirements: npm and node.
2. Clone: git clone https://<user>@bitbucket.org/raphaellab/gd3.git.
3. Install dependencies: npm install.

To use the Python scripts, you must also:

1. Clone HotNet2: git clone https://<user>@bitbucket.org/raphaellab/hotnet2.git.
2. Add "HOTNET" environment variable: Add setenvvar HOTNET <path/to/hotnet2/checkout> to ~/.environment

Visualization scripts

Mutation Matrix(js/mutation-matrix.js)

Subnetworks(js/subnetwork.js)

Transcript Plot(js/transcript-plot.js)

Pre-defined style files.

js/default-style.js: default styles

js/pancancer-sample-coloring.json: cancer type -> color mapping for PanCancer

Python scripts for saving visualizations to SVG.

Python Mutation Matrix (drawMutationMatrix.py)

Usage: see python drawMutationMatrix.py -h

Node.js scripts for saving visualizations to SVG.

Mutation Matrix(drawMutationMatrix.js)

Usage: node drawMutationMatrix.js --json=</path/to/json> --outdir=</path/to/output>

Transcript Plot(drawTranscriptPlot.js)

Usage: node drawTranscriptPlot.js --json=</path/to/json> --outfile=</path/to/output/file>