Skip to main content

MultiWiggleAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the wiggle plugin. View source.

Example usage

The bigWigs shorthand: a plain array of BigWig URLs, one subtrack each (the subtrack name is derived from the filename):

{
  type: 'MultiQuantitativeTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'MultiWiggleAdapter',
    bigWigs: [
      'https://example.com/sample1.bw',
      'https://example.com/sample2.bw',
    ],
  },
}

Preloading per-subtrack metadata: use subadapters instead of bigWigs to attach a name, a color, and a group to each subtrack. The extra keys ride along as source metadata — group drives the sidebar clustering tree and color sets the subtrack's line/fill on load:

{
  type: 'MultiQuantitativeTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'MultiWiggleAdapter',
    subadapters: [
      {
        type: 'BigWigAdapter',
        name: 'Alpha',
        group: 'Islet',
        color: '#e6194b',
        bigWigLocation: { uri: 'https://example.com/alpha.bw' },
      },
      {
        type: 'BigWigAdapter',
        name: 'Beta',
        group: 'Islet',
        color: '#f58231',
        bigWigLocation: { uri: 'https://example.com/beta.bw' },
      },
    ],
  },
}

Per-subtrack metadata from a table: the first column of samplesTsvLocation names each subtrack as the adapter does (for bigWigs, the filename without its extension), and the other columns ride along as source metadata. The track shows only the subtracks the table lists:

{
  type: 'MultiQuantitativeTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'MultiWiggleAdapter',
    bigWigs: [
      'https://example.com/sample1.bw',
      'https://example.com/sample2.bw',
    ],
    samplesTsvLocation: { uri: 'https://example.com/samples.tsv' },
  },
}

See the Config slots section below for all available configuration fields.

combines multiple BigWig files into a single multi-row quantitative track

Config slots

These slots go inside the track's adapter: "adapter": { "type": "MultiWiggleAdapter", ... }. This adapter has no uri shorthand — give it the location slots below. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
subadapters
frozen = []		array of subadapter JSON objects
bigWigs
stringArray = []		array of BigWig URLs/paths, alternative to the subadapters slot
baseUri
string = ''		what relative bigWigs URLs resolve against, stamped from the location the config was loaded from
advanced
samplesTsvLocation
maybeFileLocation		optional tab-separated table of per-sample metadata. It needs a header row, and its first column is the sample name exactly as the adapter spells it: a VCF sample, a MultiWiggle subtrack's name, a MAF species id. Every other column (population, tissue, ...) becomes an attribute of that sample, which the multi-row displays group, sort, color and tooltip rows by; a MAF adapter reads the label, color and assemblyName columns onto its species rows, over its samples entries. The table also narrows the adapter's samples to the ones it lists, and a table naming none of them is an error. An adapter that lists no samples of its own (a MAF track discovering its species from the file) takes the table's rows as its samples