Embeddable genomic visualization component based on the Integrative Genomics Viewer
npm install igvigv.js is an embeddable interactive genome visualization component developed by the
Integrative Genomics Viewer (IGV) team.
James T Robinson, Helga Thorvaldsdottir, Douglass Turner, Jill P Mesirov, igv.js: an embeddable JavaScript
implementation of the Integrative Genomics Viewer (IGV), Bioinformatics, Volume 39, Issue 1, January 2023,
btac830, https://doi.org/10.1093/bioinformatics/btac830
Below are examples and a quickstart guide. See the developer documentation for more documentation.
Mutation Annotation Format (MAF)
Pre-built files for script include, AMD, or CJS module systems (igv.min.js) and an ES6 module (igv.esm.min.js)
can be downloaded from https://cdn.jsdelivr.net/npm/igv@3.7.3/dist/.
To import igv as an ES6 module
``javascript`
import igv from "https://cdn.jsdelivr.net/npm/igv@3.7.3/dist/igv.esm.min.js"
Or as a script include (defines the "igv" global)
`html` `
Alternatively you can install with npm
npm install igv`
and source the appropriate file for your module system (igv.min.js or igv.esm.min.js) in node_modules/igv/dist.
To create an igv.js browser supply a container div
and an initial configuration defining the reference genome, initial tracks, and other state to the
function `igv.createBrowser(div, config)`.
This function returns a promise for an igv.Browser object which can used to control the browser. For example, to open
a browser on a single alignment track opened at a specific locus:
`
var igvDiv = document.getElementById("igv-div");
var options =
{
genome: "hg38",
locus: "chr8:127,736,588-127,739,371",
tracks: [
{
"name": "HG00103",
"url": "https://s3.amazonaws.com/1000genomes/data/HG00103/alignment/HG00103.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram",
"indexURL": "https://s3.amazonaws.com/1000genomes/data/HG00103/alignment/HG00103.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram.crai",
"format": "cram"
}
]
};
igv.createBrowser(igvDiv, options)
.then(function (browser) {
console.log("Created IGV browser");
})
`
Full documentation of the igv.js API is available at https://igv.org/doc/igvjs/.
Building igv.js and running the examples require Linux or MacOS. Other Unix environments will probably
work but have not been tested.
Windows users can use Windows Subsystem for Linux.
Building igv.js and running the examples requires node.js.
Development can be done directly from the source files by importing igv.js from `js/index.js`. `
See the html files in the dev` folder for examples of how to import igv.js from the source`
directory. The dist`files are not required for development, however you must build at least `
once to compile the CSS and create the required file js/embedCss.js`.
` `
git clone https://github.com/igvteam/igv.js.git
cd igv.js
npm install
npm run build
This creates a dist folder with the following files
* igv.js - UMDS file for script include, AMD, or CJS modules. A script include will define an "igv" global.
* igv.min.js - minified version of igv.js
* igv.esm.js -- ES6 module
* igv.esm.min.js -- minified version of igv.esm.js
Additionally the file `embedCSS.js` is created in the `js` folder. This contains the CSS required for igv.js,
which is injected into a shadow root containing igv.js.
To run the tests from the command line
``
npm run test
To run the examples install http-server.
Start http-server from the project root directory
`bash``
npx http-server
Then open http://localhost:8080/examples in a web browser.
igv.js require a modern web browser with support for Javascript ECMAScript 2015 (ES6).
igv.js is MIT licensed.