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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.

Example usage

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

The canvas feature displays' color setting: 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 constant; the object binds the field, and scale: "none" beside a field paints the constant while keeping the field for the way back. scale: "identity" leaves each feature its own color, a file's itemRgb or what a value callback returns, and names the colors domain lists in the key.

Config slots

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
title
maybeString		The heading of the key this scale draws, naming what the color measures. Three states: unset, the key keeps the display's own heading, usually the field's name; some text is that text; "" is a key with no title, and the only spelling of one. null reads as unset, as it does in every slot.
value
maybeColor		A CSS color, or a jexl callback over feature returning one. Writing color: "red" or color: "jexl:…" lands here. Unset, a feature's own BED itemRgb paints it if it has one, else goldenrod.
callback args: feature
field
featureField = ''		a feature field, or a jexl expression over feature, whose values each paint 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 domain or range says otherwise
scale
maybeStringEnum		none paints value and keeps the field for a switch back; categorical 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 none does, and the key names the colors in domain; unset is linear for score and categorical for any other field
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
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; under linear or log the ramp's stops, winning over scheme
labels
stringArray = []		key label for each domain value, one each in order, or under threshold for each interval from the lowest; one past the list keeps its own name
scheme
maybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue, blueyellowred)		a named ramp: a linear or log scale runs along it, and a threshold that writes cuts takes one color per interval from end to end; range's colors, where it lists any, win over it
reverse
boolean = false		turns the ramp round, so its last color paints the bottom of a linear or log domain or a threshold's lowest interval
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
domainMin
maybeNumber		the bottom of a linear or log scale's domain; unset follows the loaded values
domainMax
maybeNumber		the top of a linear or log scale's domain; unset follows the loaded values
domainQuantile
number = 1		the quantile an open end of a linear or log scale follows over the loaded values: 1 their extremes, 0.99 clips the outermost 1% at each end, each sign measured on its own
advanced