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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:

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:

Client

  1. Make sure you load this track prior to hglib.js. For example:
<script src="/higlass-transcripts.js"></script>
<script src="hglib.js"></script>
<script>
  ...
</script>

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:

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

$ 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:

npm link higlass

Commands

  • Developmental server: npm start
  • Production build: npm run build