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LDColor

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

The LD display's encoding.color paints the statistic the cells show, r2 or dprime, through a linear scale onto a named scale.scheme. An unset scheme is the metric's own, reds for r² and blues for D'. The domain is the statistic's 0 to 1 rather than the loaded values', so one r² paints one color on every track; scale.domainMin and scale.domainMax narrow it. A threshold scale paints each interval between its domain cuts one range color instead, so the triangle can take the bins a GWAS track's LD coloring uses. The slots are the shared color channel's, so jbrowse validate and "Edit plot..." judge them as they judge any other display's. A string is the field. There is no value: every cell paints its statistic through MatrixRampMixin's ramp, which has no constant color.

Example usage

{
  type: 'LDTrackDisplay',
  encoding: {
    color: { field: 'dprime', scale: { scheme: 'viridis', domainMin: 0.2 } },
  },
}

LocusZoom's r² bins, the GWAS track's, highest first in the key:

{
  type: 'LDTrackDisplay',
  encoding: {
    color: {
      field: 'r2',
      scale: {
        type: 'threshold',
        domain: [0.2, 0.4, 0.6, 0.8],
        range: ['#357ebd', '#46b8da', '#5cb85c', '#eea236', '#d43f3a'],
      },
      legend: { descending: true },
    },
  },
}

Preset fields

A field named here paints through its own scale while scale.type is unset, and range and names index its levels in order while domain is unwritten.

Field Scale Levels Names Other defaults
r2 linear scheme: reds; key "R²"
dprime linear scheme: blues; key "D'"

Config slots

A setting written to it replaces it whole: a member left out returns to its default. 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.

Slot Description
field
stringEnum (r2, dprime) = 'r2'		 The file column the cells show: r2 (R², the R2/PHASED_R2 column) or dprime (D', the DP/ABS_DPRIME one). A file with only one of the two uses that one whichever is asked for, and the legend and the menu show which.
scale
LDColorScale sub-schema		 The ramp the statistic runs along, or the intervals it is cut into, Vega-Lite's scale object. range colors a threshold's intervals only: MatrixRampMixin builds the ramp from scheme and reverse alone (Colin, 2026-10-30).
scale.type
maybeStringEnum (linear, threshold)		 linear, the default, runs the statistic along the scheme; threshold paints each interval between the domain's cuts one range color
scale.domain
stringArray = []		 a threshold scale's cuts, each the lowest value of the interval above it
scale.range
colorArray = []		 a threshold scale's colors, one per interval from the lowest; an interval left unnamed samples the scheme
scale.scheme
maybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue, redyellowblue)		 the named ramp the statistic runs across; unset is the field's own, reds for r2 and blues for dprime
scale.reverse
maybeBoolean		 Unset turns round viridis, magma, inferno and cividis, which run dark at their low end, since an unpainted cell is the page behind the matrix.
scale.domainMin
maybeNumber		 the value the bottom color paints, everything below it too; unset is 0
scale.domainMax
maybeNumber		 the value the top color paints, everything above it too; unset is 1
scale.domainMid
maybeNumber		 The value the ramp's middle stop sits at; unset, the stops spread evenly across the domain.
legend
LDColorLegend sub-schema		 The key this channel draws: title replaces the metric's name, and "" draws none; descending lists a threshold's intervals highest first.
legend.descending
maybeBoolean		 threshold key lists the highest interval first; unset follows the field's preset, else the lowest first
legend.title
maybeString		 key title; unset keeps the display's own heading, "" draws none