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.
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
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.
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
HiGlass provides an API for controlling the component from with JavaScript. Below is a minimal working example to get started and the complete documentation is availabe at docs.higlass.io.
<!DOCTYPE html>
<head>
<meta charset="utf-8">
<title>Minimal Working Example · HiGlass</title>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<link rel="stylesheet" href="https://unpkg.com/higlass@1.6.6/dist/hglib.css">
<style type="text/css">
html, body {
width: 100vw;
height: 100vh;
overflow: hidden;
}
</style>
<script crossorigin src="https://unpkg.com/react@16/umd/react.production.min.js"></script>
<script crossorigin src="https://unpkg.com/react-dom@16/umd/react-dom.production.min.js"></script>
<script crossorigin src="https://unpkg.com/pixi.js@5/dist/pixi.min.js"></script>
<script crossorigin src="https://unpkg.com/react-bootstrap@0.32.1/dist/react-bootstrap.min.js"></script>
<script crossorigin src="https://unpkg.com/higlass@1.6.6/dist/hglib.min.js"></script>
</head>
<body></body>
<script>
const hgApi = window.hglib.viewer(
document.body,
'https://higlass.io/api/v1/viewconfs/?d=default',
{ bounded: true },
);
</script>
</html>
HiGlass is provided under the MIT License.
v1.7.2
bounded into a new property called sizeMode. There are now 4 different size modes, which determine the visible height of the HiGlass instance:
default: the height is given by the sum of the tracks' heightsbounded: tells the HiGlass component to bind the height to the parent container by dynamically adjusting the height of center tracks.scroll: will activate scrolling by stretching HiGlass' drawing surface to the extent of parent DOM element and hiding overflowing content in the x direction and allowing to scroll when content overflows in the y direction.overflow: same as scroll except that you can't scroll. This mode is only needed when you want to dynamically switch between scrolling and pan+zooming.FAQs
HiGlass Hi-C / genomic / large data viewer
The npm package higlass receives a total of 847 weekly downloads. As such, higlass popularity was classified as not popular.
We found that higlass demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 0 open source maintainers collaborating on the project.
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