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Nucleotide sequence track for HiGlass
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higlass/higlass-sequence
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Display nucleotide sequences in HiGlass!
Note: This is the source code for the sequence 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
npm install higlass-sequenceThe live script can be found at:
- Make sure you load this track prior to
hglib.js. For example:
<script src="/higlass-sequence.js"></script><script src="hglib.js"></script><script> ...</script>- higlass-sequence can load sequence data in two ways:
- Convert a FASTA file into the multivec format. Use this format if you need aggregation on lower zoom levels. See the
colorAggregationModeoption below. The scriptscripts/fasta_to_hdf5.pywill convert your FASTA file into the hdf5 format which then can be converted to the multivec format (see theHiGlass docs for more information). After ingesting the multivec file into a HiGlass server, you can configure the track in your view config in the usual way, using aserverandtilesetUid:
{ "server": "http://localhost:8001/api/v1", "tilesetUid": "ScrlBGMbR_WJ0fzKXxKFzA", "uid": "seq_multivec_example", "type": "horizontal-sequence", "options": { ... }, "width": 568, "height": 25},- The sequence track can also load the data directly into the client using indexed FASTA files. No running HiGlass server is required in this case. The only additional data required (besides the FASTA file) is a
faiindex file and a chrom sizes file. The track then can be configured in the following way:
{ "uid": "seq_fasta_example", "type": "horizontal-sequence", "data": { "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" }, "options": { ... }, "width": 568, "height": 25},Using indexed FASTA files is easier and faster than multivec files. If no aggregation is needed, this is the preferred way to load data in higlass-sequence.
For an example, seesrc/index.html.
- The following options are available:
{ "colorAggregationMode": "none", // ['none', 'max', 'weighted']. Ignored when using indexed FASTA files. Determines how pixels are colored on lower zoom levels. 'max' colors the pixels according to the nucleotide with the highest occurence. 'weighted' uses a weighted interpolation of colors. "extendedPreloading": false, // More tiles than necessary are loaded. Leads to a smoother horizontal scrolling especially for multivec files. "labelPosition": "topLeft", "labelColor": "black", "labelTextOpacity": 0.4, "notificationText": "Zoom in to see nucleotides...", // Notification text if colorAggregationMode == "none" and user zooms out too far. "trackBorderWidth": 0, "trackBorderColor": "white", "backgroundColor": "white", "barBorder": true, "barBorderColor": "white", "fontSize": 16, // size of the letters "fontFamily": "Arial", "fontColor": "white", "colorScale": [ "#007FFF", // color of A "#e8e500", // color of T "#008000", // color of G "#FF0038", // color of C "#800080", // color of N "#DCDCDC", // color of everything else ], }We also build out ES modules for usage by applications who may need to import or usehiglass-sequence as a component.
Whenever there is a statement such as the following, assuminghiglass-sequence is in your node_modules folder:
import{SequenceTrack}from'higlass-sequence';
Then SequenceTrack would automatically be imported from the./es directory (set via package.json's"module" value).
For questions, please either open an issue or ask on the HiGlass Slack channel athttp://bit.ly/higlass-slack
To run the test suite:
npm run test-watch$ git clone https://github.com/higlass/higlass-sequence.git$cd higlass-sequence$ npm installIf you have a local copy of higlass, you can then run this command in the higlass-sequence directory:
npm link higlass
- Developmental server:
npm start - Production build:
npm run build
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Nucleotide sequence track for HiGlass