juicebox.js
v2.4.9
Published
juicebox.js is an embeddable interactive contact map viewer for .hic files written in JavaScript and CSS. It is based on the desktop Juicebox visualization application.
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juicebox.js
juicebox.js is an embeddable interactive contact map viewer for .hic files written in JavaScript and CSS. It is based on the desktop Juicebox visualization application.
Installation
Requirements:
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css">
Juicebox CSS
<link rel="stylesheet" type="text/css" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/juicebox.css">
Juicebox javascript -- see below
To import juicebox as an ES6 module
import juicebox from "https://cdn.jsdelivr.net/npm/[email protected]/dist/juicebox.esm.js";
Or as a script include (defines the "juicebox" global)
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/juicebox.min.js"></script>
Alternatively you can install with npm
npm install juicebox
and source the appropriate file for your module system (juicebox.min.js or juicebox.esm.js) in node_modules/juicebos.js/dist. Or build from source (see Development section below).
Usage
To create an juicebox instance call juicebox.init
with a container div and an initial configuration object as
illustrated below.
juicebox.init(container, config)
.then(function (hicBrowser) {
console.log("Juicebox loaded");
})
Configuration config
object examples follow
- A minimal juicebox config containing only a hic map with all default settings (see examples/juicebox-minimal):
const config = {
"url": "https://hicfiles.s3.amazonaws.com/hiseq/gm12878/dilution/combined.hic",
}
- Juicebox config with contact map, gene annotations, CTCF wig track, and 2D annotations (see examples/juicebox.html):
const config = {
"url": "https://hicfiles.s3.amazonaws.com/hiseq/gm12878/dilution/combined.hic",
"name": "Combined",
"locus": "18:28,504,357-29,748,974 18:28,504,357-29,748,974",
"normalization": "VC_SQRT",
"backgroundColor": "255,255,255",
"colorScale": "60,255,0,0",
"tracks": [
{
"url": "https://www.encodeproject.org/files/ENCFF144KUK/@@download/ENCFF144KUK.bigWig",
"type": "wig",
"format": "bigwig",
"name": "Homo sapiens GM12878 CTCF "
"color": "green"
},
{
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeq.txt.gz",
"type": "annotation",
"format": "refgene",
"name": "Refseq Genes",
},
{
"url": "https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined_peaks.txt",
"name": "Rao & Huntley et al. | Cell 2014 | GM12878 combined loops"
},
{
"url": "https://hicfiles.s3.amazonaws.com/hiseq/hap1/in-situ/combined_peaks.txt",
"name": "Sanborn & Rao et al. | PNAS 2015 | Hap1 loops",
"color": "#fffa03",
"displayMode": "upper"
},
{
"url": "https://hicfiles.s3.amazonaws.com/external/mumbach/GSE80820_HiChIP_GM_cohesin_peaks.txt",
"name": "Mumbach Rubin Flynn et al. | Nature Methods 2016 | GM12878 cohesin combined loops",
"color": "#000000",
"displayMode": "lower"
}
]
}
API
The juicebox.init function returns a promise for a HICBrowser object. This object exposes functions for interacting with the viewer including
- loadHicFile({url: urlString, name: string})
- loadTracks([array of track configs...])
For a description of track configurations see the documentation for igv.js. Example of a basic track configuration object:
See examples/juicebox-api.html for an example of using the API to load hicfiles and tracks.
Development
Requirements
Building juicebox.js requires Linux or MacOS, and node.js.
Other Unix environments will probably work but have not been tested. Windows users can use Windows Subsystem for Linux.
Building
git clone https://github.com/igvteam/juicebox.js.git
cd juicebox.js
npm install
npm run build
This creates a dist folder with the following files
- juicebox.js - ES5 compatible file. A script include will define the "juicebox" global.
- juicebox.min.js - minified version of juicebox.js
- juicebox.esm.js -- ES6 module
- css -- folder containing required css file juicebox.css and associated images
Supported Browsers
juicebox.js require a modern web browser with support for Javascript ECMAScript 2015.
Juicebox-web
For an out-of-the box web application for viewing and sharing contact maps from .hic files see Juicebox-web, a web application embedding a juicebox.js viewer.
License
juicebox.js is MIT licensed.