ChordSyntenyDisplay

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the circular-view plugin. View source.

Draws a SyntenyTrack in a CircularView, with a ribbon joining the two spans of each alignment.

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 circular view's encoding.color, encoding.opacity and filter decide which ribbons draw and in what color, as in the linear synteny view; 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',
    },
  ],
}

Related links#

• Adapter: BlastTabularAdapter
• Adapter: ChainAdapter
• Adapter: DeltaAdapter
• Adapter: MashMapAdapter
• Adapter: MCScanAnchorsAdapter
• Adapter: MCScanBlocksAdapter
• Adapter: MCScanSimpleAnchorsAdapter
• Adapter: MultiGenomeIndexedPAFAdapter
• Adapter: MultiGenomePAFAdapter
• Adapter: MultiPairwiseSyntenyAdapter
• Adapter: PAFAdapter
• Adapter: PairwiseIndexedPAFAdapter
• State model: runtime API
• User guide: Circular genome view
• Config guide: Synteny track
• Config guide: Tracks
• Developer guide: Custom track and display types

Config slots#

Display 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.