https://github.com/higlass/higlass-transcripts
Gene transcripts track for HiGlass
https://github.com/higlass/higlass-transcripts
Last synced: about 1 year ago
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Gene transcripts track for HiGlass
- Host: GitHub
- URL: https://github.com/higlass/higlass-transcripts
- Owner: higlass
- License: mit
- Created: 2020-05-22T13:55:18.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2023-01-11T21:53:45.000Z (over 3 years ago)
- Last Synced: 2025-03-25T19:40:38.171Z (about 1 year ago)
- Language: JavaScript
- Size: 2.32 MB
- Stars: 6
- Watchers: 1
- Forks: 2
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# HiGlass Transcripts Track
Display gene transcripts in HiGlass!
Zoomed out:
Zoomed in:
**Note**: This is the source code for the transcripts 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-transcripts
```
## Data preparation
To extract trancript data from a Gencode GTF file, the following script can be used (make sure to adjust the file names in the script)
```
python /scripts/extract_transcript_data.py
```
To create an aggregated `beddb` file from that data, you can use the script
```
python /scripts/aggregate_transcripts.py
```
Example `bed` and `beddb` files can be found in the `examples` folder.
To ingest the data into higlass-server:
```
python manage.py ingest_tileset --filename data/transcripts.beddb --filetype beddb --datatype gene-annotation --uid aweseome_transcripts
```
## Usage
The live script can be found at:
- https://unpkg.com/higlass-transcripts/dist/higlass-transcripts.js
### Client
1. Make sure you load this track prior to `hglib.js`. For example:
```
...
```
### Options
The following options are available:
```
{
"server": "http://localhost:8001/api/v1",
"tilesetUid": "awesome_transcripts",
"uid": "awesome_transcripts_uid",
"type": "horizontal-transcripts",
"options": {
"fontSize": 9, // font size for labels and amino acids (if available)
"fontFamily": "Helvetica",
"labelFontColor": "#333333",
"labelBackgroundPlusStrandColor": "#ffffff",
"labelBackgroundMinusStrandColor": "#ffffff",
"labelStrokePlusStrandColor": "#999999",
"labelStrokeMinusStrandColor": "#999999",
"plusStrandColor": "#bdbfff", // color of coding parts of the exon on the plus strand
"minusStrandColor": "#fabec2", // color of coding parts of the exon on the negative strand
"utrColor": "#C0EAAF", // color of untranslated regions of the exons
"backgroundColor": "#ffffff", // color of track background
"transcriptHeight": 12, // height of the transcripts
"transcriptSpacing": 2, // space in between the transcripts
"name": "Gene transcripts",
"maxTexts": 50, // Maximum number of labels shown on the screen
"showToggleTranscriptsButton": true, // If the "Show fewer transcripts"/"Show more transcripts" is shown
"trackHeightAdjustment": "automatic", // if "automatic", the height of the track is adjusted to the number of visible transcripts.
"startCollapsed": false, // if true, only one transcript is shown
"sequenceData": { // If this is set, transcribed amino acids are displayed when sufficiently zoomed in
"type": "fasta",
"fastaUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa",
"faiUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa.fai",
"chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes"
},
},
"width": 768,
"height": 40
}
```
### ECMAScript Modules (ESM)
We also build out ES modules for usage by applications who may need to import or use `higlass-transcripts` as a component.
Whenever there is a statement such as the following, assuming `higlass-transcripts` is in your node_modules folder:
```javascript
import { TranscriptsTrack } from 'higlass-transcripts';
```
Then `TranscriptsTrack` would automatically be imported from the `./es` directory (set via package.json's `"module"` value).
## Support
For questions, please either open an issue or ask on the HiGlass Slack channel at http://bit.ly/higlass-slack
## Development
### Testing
To run the test suite:
```
npm run test-watch
```
### Installation
```bash
$ git clone https://github.com/higlass/higlass-transcripts.git
$ cd higlass-transcripts
$ npm install
```
If you have a local copy of higlass, you can then run this command in the higlass-transcripts directory:
```bash
npm link higlass
```
### Commands
- **Developmental server**: `npm start`
- **Production build**: `npm run build`