Skip to main content

LinearPairedArcDisplay

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 VariantTrack of structural variants: each feature draws an arc from its position to its mate breakend (parsed from the VCF ALT), connecting the two loci even when the mate is on another chromosome / displayed region. Short ticks mark each breakend's mate direction; clicking an arc opens the variant details. color is jexl-evaluated per (feature, alt):

{
  type: 'VariantTrack',
  trackId: 'sv',
  name: 'Structural variants',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfTabixAdapter',
    uri: 'https://example.com/sv.vcf.gz',
  },
  displays: [
    {
      type: 'LinearPairedArcDisplay',
      displayId: 'sv-LinearPairedArcDisplay',
    },
  ],
}

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

Overview

LinearPairedArcDisplay - Identifier

Every LinearPairedArcDisplay 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": "LinearPairedArcDisplay", ... }], 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 = 'jexl:defaultPairedArcColor(feature,alt)'		the color of the arcs
callback args: feature, alt
lineWidth
maybeNumber = 3 promotable		the stroke width of the arcs, in pixels. Unset (the default) follows the session-wide default for this display type
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