LGVSyntenyDisplay

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

Example usage#

Shows a SyntenyTrack's alignments in a plain linear view (rather than the two-row synteny view). Same track config as a synteny track — just pick this display type:

{
  type: 'SyntenyTrack',
  trackId: 'hg38_vs_mm10',
  name: 'hg38 vs mm10',
  assemblyNames: ['hg38', 'mm10'],
  adapter: {
    type: 'PAFAdapter',
    uri: 'https://example.com/hg38_vs_mm10.paf',
    queryAssembly: 'hg38',
    targetAssembly: 'mm10',
  },
  displays: [
    {
      type: 'LGVSyntenyDisplay',
      displayId: 'hg38_vs_mm10-LGVSyntenyDisplay',
    },
  ],
}

Draws a SyntenyTrack's alignments in a linear genome view, stacked and colored the way an alignments display draws reads.

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
• Base config: LinearAlignmentsDisplay
• Config guide: Tracks
• Developer guide: Custom track and display types

Config slots#

These slots go on a display entry: "displays": [{ "type": "LGVSyntenyDisplay", ... }], 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.

Retired keys#

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