VariantCellColor

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

The variant display's encoding.color: the hue of every record and of every genotype cell with an alt allele, which a heterozygote paints lighter. Unset, the records paint their SV type and the cells the genotype colors. A CSS color or jexl: callback in value paints every alt cell of a variant; a field gives each of its values a color 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 or run along a linear or log ramp. A string is the field. scale.type: "identity" keys a value callback's colors: each variant paints the color it returns, and the key names the colors scale.domain lists, as on a feature track. The records paint what the cells paint, so one channel colors both, except under phaseSet, a genotype's value no record holds, where the records keep their SV type.

Example usage#

{ type: 'LinearVariantDisplay', encoding: { color: 'impact' } }

{
  type: 'LinearVariantDisplay',
  encoding: {
    color: {
      value: "jexl:get(feature,'INFO').COLOR",
      scale: {
        type: 'identity',
        domain: ['#d73027', '#4575b4'],
        names: ['Pathogenic', 'Benign'],
      },
    },
  },
}

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

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. Any other field is ordinal.

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.