higlass-arcs

Arcs Track for HiGlass

Display connections between non-adjacent regions as arcs

The WebGL implementation is inspired by Matt Deslauriers' wonderful blog post on drawing lines.

Live demo: https://higlass.github.io/higlass-arcs/

Note: This is the source code for the arcs track only! You might want to check out the following repositories as well:

• HiGlass viewer: https://github.com/higlass/higlass
• HiGlass server: https://github.com/higlass/higlass-server
• HiGlass docker: https://github.com/higlass/higlass-docker

Installation

npm install higlass-arcs

Usage

The live script can be found at:

• https://unpkg.com/higlass-arcs/dist/higlass-arcs.min.js

• Make sure you load this track prior to hglib.min.js. For example:

<script src="higlass-arcs.min.js"></script>
<script src="hglib.min.js"></script>
<script>
  ...
</script>

If you build a custom React application, import higlass-arcs in your index.js as follows:

import 'higlass-arcs'; // This import is all you have to do

import React from 'react';
import ReactDOM from 'react-dom';

import App from './App';

ReactDOM.render(<App />, document.getElementById('root'));

• Now, configure the track in your view config and be happy! Cheers 🎉

{
  ...
  {
    server: 'http://localhost:8001/api/v1',
    tilesetUid: 'my-aggregated-bedfile.beddb',
    uid: 'some-uid',
    type: '1d-arcs',
    options: {
      labelColor: 'red',
      labelPosition: 'hidden',
      trackBorderWidth: 0,
      trackBorderColor: 'black',
      name: 'Arcs for me and you!',
    },
  },
  ...
}

Take a look at src/index.html for an example. You can find the corresponding live demo at https://higlass.github.io/higlass-arcs/.

Custom Options

startField

By default, a segments x1 start value is used as the start position. You can customize this behavior by specifying another column. Useful when drawing arcs from bedpe data.

endField

By default, a segments x1 end value is used as the end position. You can customize this behavior by specifying another column. Useful when drawing arcs from bedpe data.

filter

An object with the following properties to filter segments.

Properties:

• set: a list of values that will allow segments to be included, i.e., rendered
• field: an integer defining the segment field column number that should be used to check against the set

In other words, this is how the filtering is basically implemented:

segments.filter((segment) =>
  options.filter.set.includes(segment.fields[options.filter.field])
);

Development

Installation

$ git clone https://github.com/higlass/higlass-arcs && higlass-arcs
$ npm install

Commands

Developmental server: npm start Production build: npm run build Deploy demo: npm run deploy

Changelog

v0.3.4

• Fixed arcs jumping around bug
• Fixed completelyContained option not working bug