This is the library that generates the Oncoprint visualization in cBioPortal. Essentially, it populates a canvas of a grid of m tracks of n types, where each element can either be a discrete value represented by a colored glyph on a grey background or a continuous value within a color range. Oncoprint can have many conceivable uses, but in cBioPortal, it is primarily used to visualize tracks of m genes and n patient samples, where the colored glyphs represent genomic alterations. It is also used to display a heatmap of gene and/or protein expression values for those m genes and n patient samples.
Oncoprint is on NPM. To install:
npm install --save oncoprintjs
In order to use it, just require it into your script.
const Oncoprint = require('oncoprintjs');
It can also be imported
import Oncoprint from "oncoprintjs";
A full documentation of the API is still pending, but the typescript declarations in dist/js/oncoprint.d.ts may be of use.
First, clone the repo:
git clone https://github.com/cBioPortal/oncoprintjs.git
Install the necessary NPM packages defined in package.json by running:
npm install
Next, build
npm run build
Which will write dist/oncoprint.bundle.js, which is a CommonJS module and can be included using require, or import.
The directory rules/ contains glyph styling specifications that are specific to the genomic alterations use case of Oncoprint, which you may want to use.
If you make changes to the Oncoprint code base and want to load it into the examples, do not modify oncoprint.bundle.js, since all of your code will get overwritten when compiled using npm run build. Instead, modify the files in src/ and then re-run npm run build.