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MultiWayLaneLayer

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

GC percent as bars above every lane's genes, from each genome's UCSC gc5Base bigWig added as a track:

{
  type: 'MultiWaySyntenyDisplay',
  displayId: 'hg38_liftover_multiway-MultiWaySyntenyDisplay',
  laneLayers: [
    {
      name: 'GC %',
      tracks: ['hg38-gc5Base', 'panTro6-gc5Base', 'mm39-gc5Base'],
      marks: [{ mark: 'bar', encoding: { y: 'score' } }],
    },
  ],
}

GC content computed from each genome's own sequence, one entry for every lane, a hub star's lanes on genomes the session lacks included:

{
  type: 'MultiWaySyntenyDisplay',
  displayId: 'hg38_liftOver_multiway-MultiWaySyntenyDisplay',
  laneLayers: [
    {
      name: 'GC',
      adapter: { type: 'GCContentAdapter', windowSize: 1000, windowDelta: 1000 },
      marks: [{ mark: 'bar', encoding: { y: 'score' } }],
    },
  ],
}

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

One row of data drawn in every lane through that lane's own frame, from each genome's own track, on one value scale shared by every lane.

Config slots

These slots go on a display entry: "displays": [{ "type": "MultiWayLaneLayer", ... }], 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
name
string = ''		what the layer's band is labelled
tracks
stringArray = []		the trackId each lane draws the layer from, one per genome, matched to a lane by the track's assembly. A lane no entry names draws an empty band
adapter
maybeFrozen = undefined		an adapter computing from the sequence, such as { type: 'GCContentAdapter' }, that every lane tracks names nothing for reads through its own genome. A lane reads it only while its window is under 5 Mb, since that window is the sequence it downloads, and the band's title says to zoom in past that
height
number = 24		px of band the layer takes in each lane
marks
markListSchema([{ mark: 'bar', encoding: { y: 'score' } }])		The mark display's marks, drawn over each lane's features; a mean such as a bigWig's score compares across lanes, where a count or sum reads denser on a zoomed-out lane.