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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. 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.

Example usage

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

Config slots

A setting written to it replaces it whole, since its members are alternatives: 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.

SlotDescription
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, Vega-Lite's scale object.
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 a scheme dark at its 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.type
maybeStringEnum (linear)		linear, the one scale; unset is linear