LinearWiggleDisplay

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

Example usage#

Minimal QuantitativeTrack config. See the quantitative track guide for all adapter and display options:

{
  type: 'QuantitativeTrack',
  trackId: 'coverage',
  name: 'Coverage',
  assemblyNames: ['hg38'],
  adapter: { type: 'BigWigAdapter', uri: 'https://example.com/coverage.bw' },
}

Several bigWigs stacked one per row, which is what a MultiQuantitativeTrack does by default:

{
  type: 'MultiQuantitativeTrack',
  trackId: 'coverage_by_sample',
  name: 'Coverage by sample',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'MultiWiggleAdapter',
    bigWigs: [
      'https://example.com/sample1.bw',
      'https://example.com/sample2.bw',
    ],
  },
  displayDefaults: { facet: 'source' },
}

Taller track, log scale, custom color:

{
  type: 'QuantitativeTrack',
  trackId: 'coverage',
  name: 'Coverage',
  assemblyNames: ['hg38'],
  adapter: { type: 'BigWigAdapter', uri: 'https://example.com/coverage.bw' },
  displayDefaults: {
    height: 200,
    scales: { y: { type: 'log' } },
    color: 'darkgreen',
  },
}

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

configuration for the quantitative display: an XY plot, density, line or scatter rendering of one source or of many, with facet: 'source' giving each source a row of its own

Per-source metadata (a name, color and group for each) is preloaded on the adapter rather than here — see MultiWiggleAdapter's subadapters slot, where group drives the sidebar clustering tree and color sets each source's line or fill.

These are display-level slots: set them inside a track's displays to change its defaults (setting them at the track top level has no effect). The object shorthand displayDefaults: { key: value } is equivalent to the full displays: [{ type: 'LinearWiggleDisplay', displayId: '...', key: value }] array form — see configuring displays.

Related links#

• Adapter: BedGraphAdapter
• Adapter: BedGraphTabixAdapter
• Adapter: BigWigAdapter
• Adapter: GCContentAdapter
• Extended by: SharedGCContentDisplay
• State model: runtime API
• Guide: Clustering rows
• Guide: CNV across a population (1000 Genomes)
• Guide: Cookbook
• Guide: Custom track and display types
• Guide: Display settings
• Config guide: Quantitative track
• User guide: Quantitative track
• Guide: Single-cell ATAC pseudobulk
• Guide: Structural variants (Cancer GIAB)
• Guide: Tracks

Config slots#

These slots go on a display entry: "displays": [{ "type": "LinearWiggleDisplay", ... }], or in the track's displayDefaults when this is its default display. 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.

{
  "type": "LinearWiggleDisplay",
  "defaultRendering": "density"
}

{
  "type": "LinearWiggleDisplay",
  "facet": "source"
}

{
  "type": "LinearWiggleDisplay",
  "color": { "field": "score", "scale": "threshold", "domain": [2] }
}

{
  "type": "LinearWiggleDisplay",
  "scales": { "y": { "rules": [{ "value": 30, "label": "2 copies" }, 15] } }
}