ChordVariantDisplay

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

Example usage#

The circular-view display for a VariantTrack of structural variants; translocations are drawn as chords across the circle. The three stroke slots are the chord's resting, hovered and selected colors, and each takes a jexl: expression over the feature so a chord can be colored by what it is:

{
  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',
      strokeColor: "jexl:get(feature,'INFO').SVTYPE=='BND'?'#d95f02':'rgba(255,133,0,0.32)'",
      strokeColorHover: '#555',
    },
  ],
}

How deep a chord bows toward the center is bezierRadiusRatio, a display state-model property rather than a config slot — a saved session carries it, a track config drops it.

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

Related links#

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

Config slots#

These 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.