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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 },
    },
  ],
}

Color channels

Setting Page scale.type Preset fields
encoding.color ChordColor ordinal, threshold strand, svType, impact

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.

Slot Description
mark
ChordMark		 How far each chord curves toward the center, a ChordMark object
onChordClick
maybeString		 a jexl callback run when a chord is clicked, in place of opening the record's details; unset opens the details
callback args: feature, track
encoding
ChordEncoding		 The channels each resting chord paints through: encoding.color, its line color, and encoding.opacity, its alpha.

Retired keys

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

Key On load
strokeColor moved into a current slot
strokeColorSelected ignored
strokeColorHover ignored
renderer moved into a current slot