OncoprintJS

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.

Using the Node Module

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.

Development

Getting Started

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.

Using a local version of oncoprintjs during development (e.g. in cBioPortal)

yalc (https://github.com/wclr/yalc) is extremely useful for this.

Whenever you have made a change to oncoprintjs you want to bring into another package: (1) First navigate to the oncoprint directory. Then build:

npm run build

(2) Then "publish" the package locally using yalc

yalc publish

(3) Now go to the directory of your project (e.g. cbioportal-frontend), and add the local package

yalc add oncoprintjs

(4) Install packages again, using npm or yarn. Now, you will be using your local version of oncoprintjs.

(5) When you no longer want to be using the local version of oncoprintjs, simply run

yalc remove oncoprintjs

And run npm or yarn again.

Changes to Oncoprint

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.

Schematic diagrams

oncoprintjs is written loosely with a Model-View-Controller framework, although some Views definitely have their own state.