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WiggleColor

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the wiggle plugin. View source.

Example usage

{ type: 'LinearWiggleDisplay', color: 'darkgreen' }
{
  type: 'LinearWiggleDisplay',
  color: { field: 'score', scale: 'threshold', domain: [2], range: ['#2166ac', '#b2182b'] },
}
{
  type: 'LinearWiggleDisplay',
  mark: 'heatmap',
  color: { field: 'score', scale: 'linear', scheme: 'viridis' },
}

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

The quantitative display's color: one CSS colour for every bar, or one of its two fields through a scale. score through a threshold scale is the bicolor plot — a colour each side of one cut, the origin where the domain names none, and a colour per band where it names more — and through linear a gradient across the y domain, through the y scale's own type, which colours each bar, point and density cell by its score. A line still parts in the gradient's two end colours. source through a categorical scale gives each subtrack a colour of its own, which is what several sources sharing one plot box need to be told apart. Any other pairing paints the misconfiguration grey. A wiggle colours per signal rather than per feature, so a jexl: callback over a feature has nothing to read here.

Config slots

These slots go on a display entry: "displays": [{ "type": "WiggleColor", ... }], 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		One CSS colour for every bar. Writing color: "darkgreen" lands here. Unset, the display paints the picture its layout asks for: a palette entry per source where several share one plot box, and the pos/neg pair about the origin otherwise.
field
maybeStringEnum (score, source)		score, the value each bar carries, or source, the subtrack it came from. Unset, the colour paints value.
scale
maybeStringEnum (none, categorical, linear, threshold)		how field becomes a colour: threshold paints each band between two of its cuts; linear runs range, else scheme, else viridis across the y domain through scales.y.type, with domainMid at the middle stop, colouring each bar, point and density cell by its score, and a one-colour range runs from white to that colour; a line still parts in the two end colours; categorical hands each source a colour of its own; a scale over the other field paints grey; none paints value, keeping a field for a switch back; unset beside a field, it is categorical over source and threshold over score
domain
stringArray = []		for a threshold scale, up to eight cut points, sorted, empty meaning one at the origin; for a categorical scale over source, the subtracks outside a group that take the range first, in order
range
colorArray = []		a threshold scale's colour for each band, lowest first, one more than the cuts, a missing middle band grey; the colours a categorical scale over source hands to the subtrack groups first and then to each subtrack, continuing into the default palette; a linear scale's stops, evenly spaced, one colour meaning white to it
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