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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. color is the chord's resting colour, a constant or a field of the record with a key, and colorHover and colorSelected its hovered and selected ones:

{
  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',
      color: { field: 'svType' },
      opacity: 0.45,
      colorHover: '#555',
    },
  ],
}

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

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.

SlotDescription
onChordClick
boolean = false		a jexl callback run when a chord is clicked, in place of opening the record's details
callback args: feature, track, pluginManager
color
ChordColor		The line colour of each resting chord: a CSS colour or jexl: callback, or a field of the record, svType say, whose values each take a colour with a key on the circle.
opacity
number = 1		the alpha every resting chord draws at, over its colour's own
colorSelected
color = 'black'		the line color of a chord that has been selected
callback args: feature
colorHover
color = '#555'		the line color of a chord that is being hovered over with the mouse
callback args: feature
bezierRadiusRatio
number = 0.1		how far from the center a chord across the circle passes, as a fraction of the circle's radius: 0 draws it straight through the center, and a larger value keeps every chord nearer the rim. A shorter chord bows less, in proportion to its span