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ChordSyntenyDisplay

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 SyntenyTrack: each alignment is a ribbon between the span it covers on one side and the span its mate covers on the other. The three color slots are its resting, hovered and selected fills, and each takes a jexl: expression over the feature, so anything on the record can drive the fill — here the alignment's score:

{
  type: 'SyntenyTrack',
  trackId: 'volvox_self',
  name: 'Volvox self-alignment',
  assemblyNames: ['volvox', 'volvox'],
  adapter: {
    type: 'PAFAdapter',
    uri: 'https://example.com/volvox_self.paf',
    queryAssembly: 'volvox',
    targetAssembly: 'volvox',
  },
  displays: [
    {
      type: 'ChordSyntenyDisplay',
      displayId: 'volvox_self-ChordSyntenyDisplay',
      color: "jexl:get(feature,'score')>1000?'rgba(0,0,0,0.4)':'rgba(0,0,0,0.1)'",
    },
  ],
}

The default is one flat translucent fill, since a reverse alignment already twists between its two ends. To color by strand as the linear synteny displays do:

{
  color: "jexl:get(feature,'strand')==-1?'rgba(0,0,255,0.25)':'rgba(255,0,0,0.25)'",
}

How deep a ribbon 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.

Config slots

These slots go on a display entry: "displays": [{ "type": "ChordSyntenyDisplay", ... }], 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
color
color = 'rgba(70,130,180,0.25)'		the fill color of each ribbon
callback args: feature
colorSelected
color = 'rgba(0,0,0,0.6)'		the fill color of a ribbon that has been selected
callback args: feature
colorHover
color = 'rgba(85,85,85,0.6)'		the fill color of a ribbon that is being hovered over with the mouse
callback args: feature