Skip to main content

LinearArcDisplay

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

Example usage

Selected on a FeatureTrack; each feature is drawn as one arc from its start to its end. displayMode is arcs (bezier) or semicircles. The thickness and label slots default to expressions over the feature score, so override them (plus color / arcHeight) for data without a score. All style slots are jexl-evaluated per feature:

{
  type: 'FeatureTrack',
  trackId: 'interactions',
  name: 'Interactions',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'Gff3TabixAdapter',
    uri: 'https://example.com/interactions.gff3.gz',
  },
  displays: [
    {
      type: 'LinearArcDisplay',
      displayId: 'interactions-LinearArcDisplay',
      displayMode: 'semicircles',
      color: "jexl:feature.strand==-1?'red':'blue'",
      arcHeight: 80,
      label: "jexl:feature.name",
    },
  ],
}

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

Overview

LinearArcDisplay - Identifier

Every LinearArcDisplay has a unique displayId, a required top-level field that identifies it (not one of the config slots below).

Config slots

These slots go on a display entry: "displays": [{ "type": "LinearArcDisplay", ... }], 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
color
color = 'darkblue'		the color of the arcs
callback args: feature
thickness
number = 'jexl:logThickness(feature,'score')'		the thickness of the arcs, in pixels; an arc given 0 or less is not drawn at all
callback args: feature
label
string = 'jexl:get(feature,'score')'		the label to appear at the apex of the arcs
callback args: feature
arcHeight
number = 'jexl:log10(get(feature,'end')-get(feature,'start'))*50'		the height of the arcs
callback args: feature
caption
string = 'jexl:get(feature,'name')'		the caption to appear when hovering over any point on the arcs
callback args: feature
displayMode
stringEnum (arcs, semicircles) = 'arcs'		render semi-circles instead of arcs
minScore
number = 0		hide arcs whose feature score is below this; features with no score are always drawn
height
number = 100		default height for the track
fetchSizeLimit
number = 1_000_000		maximum data to attempt to download for a given track, used if adapter doesn't specify one
advanced
forceLoad
boolean = false		Declarative equivalent of the "Force load" button on the "too much data" banner: when true the display always renders, however large the region or dense the features. Off by default (the gate guards against huge downloads). Set it on a view no one can interact with — an embedded / notebook view, or a screenshot — where the region is known and you want it drawn without a click.
advanced