HiGlass Transcripts Track

Display gene transcripts in HiGlass!

Zoomed out:

!Transcripts track

Zoomed in:

!Transcripts track

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

$3

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

`



`

$3


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
}
`

$3

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

$3

To run the test suite:

`
npm run test-watch
`




$3

`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
`

$3

- Developmental server: npm start
- Production build: npm run build`