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FeatureColor

Auto-generated from the config schema in the source — see the config guide for concepts. Built into JBrowse core. View source.

The feature displays' encoding.color: a CSS color or jexl: callback in value, or a field whose values each take a range color, whose numbers each take the color of the interval between cut points they fall in, or whose numbers run along a color ramp, with a key. A string is the field; a written field always paints. scale.type: "identity" keeps each feature's color, whether a file's itemRgb or what a value callback returns, and names the colors scale.domain lists in the key. Like UCSC's itemRgb on, it paints an itemRgb of 0,0,0 or 0 black, which otherwise reads as no color, and reads a comma-free itemRgb as a packed integer.

Example usage

{ type: 'LinearBasicDisplay', encoding: { color: { value: 'goldenrod' } } }
{
  type: 'LinearBasicDisplay',
  encoding: {
    color: { field: 'gene_biotype', scale: { range: ['#1f77b4', '#ff7f0e'] } },
  },
}
{
  type: 'LinearBasicDisplay',
  encoding: {
    color: {
      field: 'type',
      scale: {
        domain: ['prophage', 'plasmid'],
        range: ['#d95f02', '#1b9e77'],
        unknown: '#cccccc',
      },
    },
  },
}
{
  type: 'LinearBasicDisplay',
  encoding: {
    color: {
      field: 'score',
      scale: {
        type: 'threshold',
        domain: [0.5, 0.9],
        range: ['#c6dbef', '#6baed6', '#08519c'],
      },
    },
  },
}
{
  type: 'LinearBasicDisplay',
  encoding: { color: { field: 'score', scale: { scheme: 'viridis', domainMin: 0 } } },
}
{
  type: 'LinearMultiRowFeatureDisplay',
  encoding: {
    color: {
      scale: {
        type: 'identity',
        domain: ['rgb(255,0,0)', 'rgb(0,128,0)'],
        names: ['Active TSS', 'Strong transcription'],
      },
    },
  },
}

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.

FieldScaleLevelsNamesOther defaults
strandordinal1, -1, 0Forward strand, Reverse strand, No strandrange: tomato, cornflowerblue, goldenrod
svTypeordinalDEL, DUP, INS, INV, CNV, TR, BND, CPX, OTHERDeletion, Duplication, Insertion, Inversion, Copy-number variable, Tandem repeat, Breakend / translocation, Complex, Other / mixedrange: #e41a1c, #377eb8, #800080, #ff7f00, #7e6148, #e7298a, #17becf, #66a61e, #000000; key "SV type"
impactordinalHIGH, MODERATE, LOW, MODIFIER, Unannotatedrange: #d32f2f, #f57c00, #fbc02d, #9e9e9e, #607d8b; key "Consequence impact"
scorelinear

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.

SlotDescription
value
maybeColor		A CSS color, or a jexl callback over feature returning one. Unset, a feature's own BED itemRgb paints it if it has one, else goldenrod. Alignments' value is constant-only; here a callback stays, since the worker evaluates it per box, where a field reads the transcript.
callback args: feature
scale
FeatureColorScale sub-schema		How the field's values map to colors, Vega-Lite's scale object.
legend
FeatureColorLegend sub-schema		The key this channel draws.
field
featureField = ''		a feature field, or a jexl expression over feature, whose values each take one range color, with a key; a transcript and its parts paint the transcript's value, or its gene's where the transcript has none; strand paints forward tomato and reverse cornflowerblue unless scale.domain or scale.range says otherwise
scale.type
maybeStringEnum		ordinal a range color per value of field; threshold a range color per interval between the cut points in domain; linear or log a color along a ramp from domainMin to domainMax; identity paints each feature's own color, as a channel with no field does, except that an itemRgb of 0,0,0 or 0 paints black and a comma-free one reads as a packed integer, and the key names the colors in domain; unset is linear for score and ordinal for any other field
scale.domain
stringArray = []		the values that take the range first, in order; a value left out takes a color no listed value or value met before it paints, the first time the track shows it, and keeps it. Under threshold, the ascending cut points, a value on a cut taking the interval above it. Under identity, the CSS colors the key names, in order
scale.range
colorArray = []		CSS colors the domain takes, in order, continuing into the default palette past its end; under threshold one per interval, one more than the cuts, an interval left out sampling the default ramp; under linear or log the ramp's stops, winning over scheme
scale.unknown
maybeColor		color for a value missing from domain. Unset: the next palette color where the display deals one, and the levels a preset field names, such as strand's, keep their own colors. A color: that color. "": no color dealt, so a feature paints the no-value grey, a variant cell the alt hue, and a row keeps the color it already has
scale.invalid
maybeColor		color for a feature with no value under an ordinal scale's field; unset, the display's no-value color
scale.names
stringArray = []		key name for each domain value, one each in order, or under threshold for each interval from the lowest; a value past the end of the list shows its own
scale.scheme
maybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue, redyellowblue)		a named ramp: a ramp scale runs along it, a threshold that writes cuts takes one color per interval from end to end, and an ordinal scale that lists a domain one per value; range's colors, where it lists any, win over it
scale.reverse
maybeBoolean		turns the ramp round, so its last color paints the bottom of a ramp's domain or a threshold's lowest interval; unset follows the field's preset, else runs as written
scale.domainMid
maybeNumber		the value the ramp's middle stop sits at, so a diverging ramp centres somewhere other than the middle of the domain, both sides on one scale: the farther end of the domain reaches its end color and equal distances from the middle take equal colors; unset, the stops are evenly spaced across it
scale.domainMin
maybeNumber		the bottom of a ramp's domain; unset follows the loaded values
scale.domainMax
maybeNumber		the top of a ramp's domain; unset follows the loaded values
scale.domainQuantile
number = 1		the quantile an open end of a ramp follows over the loaded values: 1 their extremes, 0.99 clips the outermost 1% at each end, each sign measured on its own
advanced
legend.title
maybeString		key title; unset keeps the display's own heading, "" draws none
legend.descending
maybeBoolean		threshold key lists the highest interval first; unset follows the field's preset, else the lowest first