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SyntenyColor

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

Example usage

{ type: 'LinearSyntenyView', color: { field: 'strand' } }
{ type: 'DotplotView', color: { field: 'query' } }
{ type: 'LinearSyntenyView', color: { field: 'identity', scheme: 'magma', domainMin: 0.9 } }
{
  type: 'LinearSyntenyView',
  color: {
    field: 'gene_group',
    domain: ['A1a', 'B1'],
    range: ['#1b9e77', '#d95f02'],
    labels: ['Subgenome A', 'Subgenome B'],
    title: 'Gene group',
  },
}

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

The linear synteny and dotplot views' color setting, which every track in the view paints with: one colour for every alignment, or a field each alignment carries — its strand, the sequence at either end, the anchor assembly's, the track it came from, a measurement on its preset ramp (identity, mapq, dnds), or a column the tracks declare in attributeColumns. A string is the constant.

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
value
maybeColor		The colour of every alignment under the none scale, in place of the view's default scheme: the match block of a synteny ribbon, whose insertions and deletions keep their colours, or a dotplot point. Writing color: "grey" lands here. Unset, the default scheme paints.
field
string = ''		what colours an alignment: strand paints forward and reverse; query and target one colour per sequence on that side, reference one per chromosome of the anchor assembly across a stack, track one per overlaid track (pinned under Track colors); identity, mapq and dnds paint the preset ramps; any other name is a column the tracks declare in attributeColumns, a ramp over the values seen for numbers and one colour per label for text (or the colour a color column put beside it)
scale
maybeStringEnum (none)		none paints value and keeps the field for a switch back; unset, a field paints
domain
stringArray = []		a text column's labels that take the palette first, in order, and lead the key, the rest following sorted; a label left out takes a colour no listed label or label met before it paints, the first time the view meets it, and keeps it
range
colorArray = []		CSS colours a text column's labels take, in domain order, continuing into the default palette past its end; with no domain, each label takes one of them by its name; on a ramp (identity, mapq, dnds or a numeric column), its stops, evenly spaced, in place of the field's own
scheme
maybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue)		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
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
title
maybeString		key title; unset keeps the display's own heading, "" draws none