https://github.com/higlass/higlass-plugins
https://github.com/higlass/higlass-plugins
Last synced: 11 months ago
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- Host: GitHub
- URL: https://github.com/higlass/higlass-plugins
- Owner: higlass
- License: mit
- Created: 2021-09-22T04:09:46.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2021-11-01T04:20:09.000Z (over 4 years ago)
- Last Synced: 2025-02-27T02:18:46.129Z (over 1 year ago)
- Language: HTML
- Size: 497 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# HiGlass Plugins
A collection of popular / useful higlass plugins.
**Note**: This is the source code for the plugins 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
## Included tracks
- [higlass-pileup](https://github.com/higlass/higlass-pileup)
- [higlass-multivec](https://github.com/higlass/higlass-multivec)
- [higlass-labelled-points-track](https://github.com/higlass/higlass-labelled-points-track)
- [higlass-arcs](https://github.com/higlass/higlass-arcs)
- [higlass-transcripts](https://github.com/higlass/higlass-transcripts/)
- [higlass-dynseq](https://github.com/kundajelab/higlass-dynseq)
## Installation
```
npm install higlass-plugins
```
## Usage
The live scripts can be found at:
- https://unpkg.com/higlass-plugins/dist/higlass-plugins.min.js
### Client
1. Make sure you load this component prior to `hglib.js`. For example:
```
...
```
2. Now, configure the track in your view config and be happy!
```
{
"editable": true,
"trackSourceServers": [
"http://higlass.io/api/v1"
],
"exportViewUrl": "/api/v1/viewconfs",
"views": [
{
"initialXDomain": [
0,
100000
],
"tracks": {
"top": [
{
"type": "pileup",
"options": {
"axisPositionHorizontal": "right",
"axisLabelFormatting": "normal",
"showCoverage": false,
"colorScale": [
// A T G C N Other
"#2c7bb6",
"#92c5de",
"#ffffbf",
"#fdae61",
"#808080",
"#DCDCDC"
]
},
"height": 180,
"uid": "FylkvVBTSumoJ959HT4-5A",
"data": {
"type": "bam",
"url": "https://pkerp.s3.amazonaws.com/public/bamfile_test/SRR1770413.sorted.bam",
"chromSizesUrl": "https://pkerp.s3.amazonaws.com/public/bamfile_test/GCF_000005845.2_ASM584v2_genomic.chrom.sizes"
},
"width": 470
}
]
},
"layout": {
"w": 12,
"h": 6,
"x": 0,
"y": 0
}
}
]
}
```
## Support
For questions, please either open an issue or ask on the HiGlass Slack channel at http://bit.ly/higlass-slack
## Development
### Installation
```bash
$ git clone https://github.com/higlass/higlass-plugins && higlass-plugins
$ npm install
```
### Commands
**Developmental server**: `npm start`
**Production build**: `npm run build`