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LinearSyntenyDisplay

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

Example usage

A SyntenyTrack config to paste into tracks. The adapter needs the query (first) and target (second) assembly names, matched by the track's assemblyNames. See the synteny track guide for all options:

{
  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',
  },
}

See the Config slots section below for all available configuration fields.

Config slots

These slots go on a display entry: "displays": [{ "type": "LinearSyntenyDisplay", ... }], 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
drawCurves
maybeBoolean = false promotable		Draw each ribbon as a bezier curve rather than a straight chord. Unset (the default) follows the session-wide default for this display type, falling back to off (straight chords); an explicit true/false customizes the track. The synteny view's settings checkbox writes this slot on every level of that view, and an init spec's drawCurves key does the same for the tracks it opens
drawLocationMarkers
maybeBoolean = false promotable		Continue the query row's scalebar grid down through the ribbons: a tick at each round query coordinate, joined to the coordinate the alignment pairs it with. Unset (the default) follows the session-wide default for this display type, falling back to off; an explicit true/false customizes the track, through the same settings-menu row and init key as drawCurves above