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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. What a ribbon's colour says is the circular view's color, as in the linear synteny view, with its alpha and minAlignmentLength; these slots are the hovered and selected fills:

{
  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',
      colorHover: 'rgba(0,0,0,0.5)',
    },
  ],
}

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
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
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