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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

{
  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 — 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.

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.

SlotDescription
lineZoneHeight
number = 100		Height of the zone for connecting lines at the top
advanced
ldMetric
stringEnum (r2, dprime) = 'r2'		Which of the file's columns to draw: 'r2' (R², the R2/PHASED_R2 column) or 'dprime' (D', the DP/ABS_DPRIME one). A file that carries only one of the two serves that one whichever is asked for, and reports which through the legend.
showLegend
boolean = false		Whether to show the legend. Defaults to off.
showLDTriangle
boolean = true		Whether to show the LD triangle heatmap
squashToHeight
boolean = false		When true, squash the LD triangle to fit the display height
advanced
maxVariantSeparation
number = 0		Maximum separation, in variants, between the two SNPs of a drawn pair. Pairs further apart are dropped, which turns the matrix from n²/2 cells into n·k. This is plink's --ld-window, and a file plink wrote is usually already windowed, so it most often drops nothing. Set to 0 to draw every pair the file names.
advanced
showVerticalGuides
boolean = true		Whether to show vertical guides at the connected genome positions on hover
advanced
showLabels
boolean = false		Whether to show variant labels above the tick marks
advanced
tickHeight
number = 6		Height of the vertical tick marks at the genomic position
advanced
useGenomicPositions
boolean = false		When true, draw cells sized according to genomic distance between SNPs rather than uniform squares
advanced
height
number = 400		Starting height in pixels for the LD triangle, excluding the lineZoneHeight band; drag-resizable
Inherited from BaseLinearDisplay4 slots
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