LDTrackDisplay

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the variants plugin. View source.

Linkage disequilibrium heatmap read from an LDTrack's pre-computed file — PLINK --r2 output and the formats that follow it. JBrowse does not compute LD from genotypes; run plink (or an equivalent) and point this at the result.

Example usage#

{
  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',
      encoding: { color: { field: 'dprime' } },
      legend: { show: true },
    },
  ],
}

Overview#

LDTrackDisplay - Identifier#

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

Related links#

• Adapter: PlinkLDAdapter
• Adapter: PlinkLDTabixAdapter
• State model: runtime API
• Config guide: Tracks
• Developer guide: Custom track and display types

Config slots#

Display 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.

Retired keys#

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.