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VariantCellColor

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: 'LinearMultiSampleVariantDisplay', color: { field: 'impact' } }
{
  type: 'LinearMultiSampleVariantDisplay',
  color: {
    field: 'INFO.AF',
    scale: 'threshold',
    domain: ['0.001', '0.01', '0.05'],
    range: ['#b2182b', '#ef8a62', '#67a9cf', '#2166ac'],
  },
}

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

The multi-sample variant displays' color setting: the hue of every alt-carrying genotype cell, which shadeByDosage then lightens for a heterozygote. Unset, the cells paint the genotype colours. A CSS colour or jexl: callback in value paints every alt cell of a variant; a field gives each of its values a colour with a key. Three fields are presets: impact, the most severe SnpEff/VEP consequence tier; svType, the structural-variant class; phaseSet, the FORMAT PS block, in phased mode. Any other field is read off the record — INFO.CLNSIG, QUAL, or a jexl: expression — and a numeric one cut into intervals by a threshold scale. A string is the constant.

Config slots

These slots go on a display entry: "displays": [{ "type": "VariantCellColor", ... }], 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
value
maybeColor		A CSS colour, or a jexl callback over feature returning one, for every alt cell of the variant. Unset, the cells paint the genotype colours.
callback args: feature
field
featureField = ''		impact, the most severe SnpEff/VEP consequence tier; svType, the structural-variant class; phaseSet, the FORMAT PS block in phased mode; or any record field, INFO.CLNSIG say, or a jexl expression over feature, whose values each paint one range colour with a key. A record with no value keeps the default alt colour
scale
maybeStringEnum		none paints value and keeps the field for a switch back; categorical a range colour per value of field; threshold a range colour per interval between the cut points in domain; unset follows field
domain
stringArray = []		the values that take the range first, in order; under threshold, the ascending cut points, a value on a cut taking the interval above it
range
colorArray = []		CSS colours the domain takes, in order, continuing into the default palette past its end; under threshold one per interval, one more than the cuts