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FeatureColor

Auto-generated config schema for the current JBrowse release — 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'],
  },
}

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

The canvas feature displays' color setting: a CSS colour or jexl: callback in value, or a field whose values each take a range colour, whose numbers each take the colour of the interval between cut points they fall in, or whose numbers run along a colour 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 colour, a file's itemRgb or what a value callback returns, and names the colours domain lists in the key.

Config slots

These slots go on a display entry: "displays": [{ "type": "FeatureColor", ... }], 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
title
export const colorTitleSlot = {
  title: {
    type: 'maybeString',
    description: 'key title; unset follows field, "" draws none',
  },
} as const
The heading of the key this scale draws, naming what the colour measures. Three states: unset, the key is titled with field; 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 colour, 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 colour 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 colour per value of field; threshold a range colour per interval between the cut points in domain; linear or log a colour along a ramp from domainMin to domainMax; identity paints each feature's own colour, as none does, and the key names the colours 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 keeps a colour derived from itself that no listed value paints, so every region agrees on it. Under threshold, the ascending cut points, a value on a cut taking the interval above it. Under identity, the CSS colours the key names, in order
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; under linear or log the ramp's stops, winning over scheme
labels
stringArray = []		what the key names each domain value, one each in order, or under threshold 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)		a named ramp for a linear or log scale; range's colours, where it lists any, win over it
reverse
boolean = false		turns a linear or log scale's ramp round, so its last colour paints the bottom of the domain
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 colour and equal distances from the middle take equal colours; 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, each sign anchored at 0: 1 their extremes, 0.99 clips the outermost 1%
advanced