higlass-multi-tileset

higlass-multi-tileset

Multi-tileset data fetcher for HiGlass

Installation

If you are using NPM:

npm install higlass-multi-tileset

Then you can load it by adding this import to your JavaScript:

import MultiTilesetDataFetcher from 'higlass-multi-tileset';

// Alternatively, if you don't need programmatic access:
import 'higlass-multi-tileset';

Otherwise, load higlass-multi-tileset from a CDN. You can use this script tag:

<script src="https://unpkg.com/higlass-multi-tileset"></script>
<!-- Make sure to load higlass-multi-tileset before hglib.js -->
<script src="hglib.js"></script>

Usage

The multi tileset data fetcher can be used to fetch data from multiple tilesets at once.

{
  "data": {
    // The "type" field tells HiGlass to use this data fetcher
    "type": "multi-tileset",
    // An array of data configs 
    "configs": [
      {
        "server": "http://localhost:8001/api/v1",
        "tilesetUid": "my-bigwig-tileset",
      },
      {
        "server": "https://my-higlass-server.com/api/v1",
        "tilesetUid": "my-fasta-tileset",
        
        // The primary data config will be the source of
        // tileset info, and only tiles that exist in the
        // primary tileset will be returned.

        // Defaults to the first config specified (index 0)
        "primary": true
      },
      {
        "type": "local-tiles",
        "tilesetInfo": { ... },
        "tiles": { ... }
      }
    ]
  },
  // Other options for the track go here
  ...
}

The tiles returned from the data fetcher will have an array for the tileData property that includes the tile data from every config specified.

For example, in your track you might use:

renderTile(tile) {
  const firstTile = tile.tileData[0];
  render(firstTile.dense);
  // The second data config is the source for this tile data
  const secondTile = tile.tileData[1];
}

Features

This data fetcher comes with a special feature: tile ID filters. If you want to filter out some tile IDs from some data configs to avoid fetching them when they aren't needed, you can use the setFilter() function on the dataFetcher.

updateOptions(newOptions) {
  if (
    this.dataFetcher.constructor.config &&
    this.dataFetcher.constructor.config.type == 'multi-tileset'
  ) {
    // Applies to the primary data config (no second argument)
    this.dataFetcher.setFilter(tileId => tileId != 'banned-id');
    // Don't fetch any tiles from the second data config
    // (second argument is index)
    this.dataFetcher.setFilter(_ => false, 1);
  }
}

This can be helpful to improve performance in situations where one of the data configs is not necessary. For example, in higlass-dynseq, a filter is applied to the FASTA data config to avoid fetching the sequence unless it is visible on screen.

Support

File an issue if you have found a bug, would like help resolving a problem, or want to ask a question about using the track.

Alternatively, contact Arjun Barrett for more information.