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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',
      color: { field: 'dprime' },
      showLegend: true,
    },
  ],
}

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

Overview

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.

LDTrackDisplay - Identifier

Every LDTrackDisplay 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": "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 band above the triangle holding the connector lines and labels
advanced
color
LDColor		Which statistic the cells are, field r2 or dprime, and the linear ramp it paints through over the statistic's 0 to 1.
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		on hover, draw guides across the view at the pair's genomic positions
advanced
showLabels
boolean = false		show variant labels above the tick marks
advanced
tickHeight
number = 6		height of the tick marks at the genomic positions
advanced
variantLayout
stringEnum (genomic, columns) = 'columns'		'columns' draws every SNP one uniform square wide; 'genomic' sizes the cells by the genomic distance between SNPs. The multi-sample variant display takes the same slot for the same choice.
advanced
height
number = 400		default height of the display, the band above the triangle included
showLegend
boolean = false		show the color scale legend
squashToHeight
boolean = false		squash the triangle vertically to fill the display height instead of drawing square cells