LDTrackDisplay

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

Example usage#

The pre-computed heatmap, with the legend on so the R² ramp is labelled:

{
  type: 'LDTrack',
  trackId: 'ld',
  name: 'Linkage disequilibrium',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'PlinkLDTabixAdapter',
    uri: 'https://example.com/plink.ld.gz',
  },
  displays: [
    {
      type: 'LDTrackDisplay',
      displayId: 'ld-LDTrackDisplay',
      showLegend: true,
    },
  ],
}

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

Linkage disequilibrium heatmap read from an LDTrack's pre-computed file (e.g. PLINK --r2 output), rather than computed from genotypes. Use LDDisplay instead to compute LD from a VariantTrack's own VCF.

The genotype-derived filters the shared base declares (minorAlleleFrequencyFilter, hweFilterThreshold, callRateFilter) have nothing to act on here — the file's rows are already computed — so they are inherited but inert.

Every slot comes from the shared base below; this display adds none of its own.

Related links#

• Adapter: PlinkLDAdapter
• Adapter: PlinkLDTabixAdapter
• Base config: SharedLDDisplay
• Guide: Custom track and display types
• Guide: Defaults for all tracks
• Guide: Tracks

Config slots#

These slots go on a display entry: "displays": [{ "type": "LDTrackDisplay", ... }], 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.

'jexl:get(feature,'_mouseOver')||get(feature,'name')||get(feature,'function')||get(feature,'id')'