higlass

Introduction

HiGlass is a web-based viewer for datasets too large to view at once. It features synchronized navigation of multiple views as well as continuous zooming and panning for navigation across genomic loci and resolutions. It supports visual comparison of genomic (e.g., Hi-C, ChIP-seq, or bed annotations) and other data (e.g., geographic maps, gigapixel images, or abstract 1D and 2D sequential data) from different experimental conditions and can be used to efficiently identify salient outcomes of experimental perturbations, generate new hypotheses, and share the results with the community.

A live instance can be found at http://higlass.io. A Docker container is available for running an instance locally, although we recommend using the higlass-manage package to start, stop and configure local instances.

For documentation about how to use and install HiGlass, please visit http://docs.higlass.io.

Citation

Kerpedjiev, P., Abdennur, N., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., ... & Gehlenborg, N. HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps. Genome Biology (2018): 19:125. https://doi.org/10.1186/s13059-018-1486-1

Example

Development

To run higlass from its source code simply run the following:

npm clean-install
npm run start

This starts a server in development mode at http://localhost:8080/.

Once started, a list of the examples can be found at http://localhost:8080/examples.html. Template viewconfs located at /docs/examples/viewconfs can viewed directly at urls such as http://localhost:8080/apis/svg.html?/viewconfs/overlay-tracks.json.

Tests

The tests for the React components and API functions are located in the test directory. To save time and only run relevant tests, open karma.conf.js and select the test files to run before running test-watch.

npm run test-watch

Troubleshooting:

• If the installation fails due to sharp > node-gyp try installing the node packages using python2:

  npm ci --python=/usr/bin/python2 && rm -rf node_modules/node-sass && npm ci
  

API

HiGlass provides an API for controlling the component from within a Javascript script. Complete documentation is availabe at docs.higlass.io. Example:

<link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" type="text/css">
<link rel="stylesheet" href="https://unpkg.com/higlass@1.0.1/dist/styles/hglib.css" type="text/css">

<script src="https://cdnjs.cloudflare.com/ajax/libs/react/15.6.2/react.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/react-dom/15.6.2/react-dom.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/pixi.js/4.6.2/pixi.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/react-bootstrap/0.31.0/react-bootstrap.min.js"></script>
<script src="https://unpkg.com/higlass@1.0.1/dist/scripts/hglib.js"></script>

<div
    id="development-demo"
    style="position: absolute; left: 1rem; top: 1rem; bottom: 1rem; right: 1rem">
</div>

<script>
const api = hglib.createHgComponent(
    document.getElementById('development-demo'),
    'http://higlass.io/api/v1/viewconfs/?d=default',
    { bounded: true }
);
</script>

Related

• HiGlass Manage - Easy to use interface for deploying a local HiGlass instance
• HiGlass Docker - Build an image containing all the components necessary to deploy HiGlass
• HiGlass Server - Server component for serving multi-resolution data
• HiGlass App - The code for the web application hosted at http://higlass.io

License

HiGlass is provided under the MIT License.

Changelog

v1.6.4

• Truly fix #593: zoom to data extent when adding the first track to an empty view

Detailed changes since v1.6.3