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MafColor

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

Example usage

{ type: 'LinearMafDisplay', color: 'identity' }
{ type: 'LinearMafDisplay', color: 'identity', y: 'identity' }
{
  type: 'LinearMafDisplay',
  color: { field: 'identity', domainMin: 0.7, scheme: 'viridis' },
}

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

The MAF display's color: what colours each species row's aligned cells. mismatch paints a base only where it differs from the reference, base every base, identity the mean identity to the reference along a ramp, chromosome each block by the rank of its source chromosome within the row, and codon each codon by its amino-acid change, given an annotationAdapter. A string is the field. Each field has one scale: identity runs from domainMin 0 to domainMax 1 along the redgreyblue scheme, and the others are categorical. The bases and the codons paint the theme's colours. The slots are the shared colour object's, so jbrowse validate and "Edit plot..." judge them as they judge any other display's.

Config slots

These slots go on a display entry: "displays": [{ "type": "MafColor", ... }], 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
field
stringEnum (mismatch, base, identity, chromosome, codon) = 'mismatch'		what colours a cell: mismatch, base, identity, chromosome or codon
domain
stringArray = []		the values the key lists, in order: under chromosome each rank from 0, the main source chromosome; under codon nonsyn, syn and stop
range
colorArray = []		CSS colours: under chromosome one per rank from the main source chromosome, the last painting every rank past it; under identity the ramp's stops, winning over scheme; the bases and the codons paint the theme's colours
labels
stringArray = []		what the key names each domain value, one each in order; one past the list keeps its own name
title
maybeString		key title; unset is the field's own heading, "" draws none
scheme
maybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue)		the named ramp identity runs along; unset is redgreyblue, and range's colours, where it lists any, win over it
reverse
boolean = false		turns the identity ramp round, so its last colour paints the low end
domainMin
maybeNumber		the identity the ramp's low end paints, 0 to 1; unset is 0, and 0.7 spreads the ramp over close relatives
domainMax
maybeNumber		the identity the ramp's high end paints; unset is 1
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