ChordVariantDisplay

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the circular-view plugin. View source.

Draws the structural variants of a VariantTrack in a CircularView, each translocation as a chord across the circle.

Example usage#

The circular-view display for a VariantTrack of structural variants; translocations are drawn as chords across the circle. encoding.color is the chord's resting color, a constant or a field of the record with a key; a hovered chord darkens it and a selected one takes the theme's highlight:

{
  type: 'VariantTrack',
  trackId: 'sv',
  name: 'Structural variants',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfTabixAdapter',
    uri: 'https://example.com/sv.vcf.gz',
  },
  displays: [
    {
      type: 'ChordVariantDisplay',
      displayId: 'sv-ChordVariantDisplay',
      encoding: { color: 'svType' },
      opacity: 0.45,
    },
  ],
}

Related links#

• Adapter: BedpeAdapter
• Adapter: SplitVcfTabixAdapter
• Adapter: StarFusionAdapter
• Adapter: VcfAdapter
• Adapter: VcfTabixAdapter
• State model: runtime API
• User guide: Circular genome view
• Config guide: Tracks
• Developer guide: Custom track and display types

Config slots#

Display slots go on a display entry: "displays": [{ "type": "ChordVariantDisplay", ... }], 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.

Retired keys#

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.