raphael-group/gd3

Name: gd3

Owner: raphael-group

Description: Javascript library for visualizing genomics data with D3.

Created: 2014-01-03 22:52:50.0

Updated: 2017-11-14 04:20:07.0

Pushed: 2017-01-06 15:08:01.0

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Size: 1344

Language: JavaScript

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README

gd3

A library of genomics visualizations.

Setup
  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
Javascript: (js/)

Visualization scripts

Mutation Matrix(js/mutation-matrix.js)

Subnetworks(js/subnetwork.js)

Transcript Plot(js/transcript-plot.js)

Styles (js/style/)

Pre-defined style files.

js/default-style.js: default styles

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

Draw (.)

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>
This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.