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.

Draws a SyntenyTrack's alignments in a linear genome view, stacked and colored the way an alignments display draws reads. It has the alignments display's bands and settings but the sashimi band, the junction filter fields, pileup.bases and modifications: a synteny block has no introns, basecaller tags or qualities.

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',
    },
  ],
}

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: BaseLinearAlignmentsDisplay
• Config guide: Tracks
• Developer guide: Custom track and display types

Config slots#

Display 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.