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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.

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
Inherited from BaseLinearDisplay8 slots
maxFeatureScreenDensity
number = 1		maximum features per pixel before showing a "too many features" message
advanced
height
number = 100		default height for the track
mouseover
string = 
'jexl:get(feature,'_mouseOver')||get(feature,'name')||get(feature,'function')||get(feature,'id')'
text to display when the cursor hovers over a feature
callback args: feature
jexlFilters
stringArray = []		config jexlFilters are deferred evaluated so they are prepended with jexl at runtime rather than being stored with jexl in the config
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
densityTier
stringEnum (auto, features, density) = 'auto'		when to draw the features-per-bin density band in place of features: "auto" swaps to it where the region is too large to fetch, "features" never does and keeps the banner, "density" always does. Needs a density source on the adapter (its densityAdapter slot)
advanced
densityTierBpPerPx
number = 0		in "auto" mode, also draw the density band from this many bp per pixel outward, before the region is too large to fetch; 0 leaves the swap to the fetch-size gate alone
advanced