higlass-arcs
v0.3.4
Published
Arc tracks for HiGlass
Downloads
188
Readme
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., renderedfield
: an integer defining the segment field column number that should be used to check against theset
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