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SyntenyColor

Auto-generated from the config schema in the source — 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: 'identity', scale: 'threshold', domain: ['0.95', '0.99'] } }
{
  type: 'LinearSyntenyView',
  color: {
    field: 'gene_group',
    domain: ['A1a', 'B1'],
    range: ['#1b9e77', '#d95f02'],
    labels: ['Subgenome A', 'Subgenome B'],
    title: 'Gene group',
  },
}

The linear synteny and dotplot views' color setting, which every track in the view paints with: one color 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 through its preset (identity and dnds on a ramp, mapq in the alignments display's bins, syntenicDepth grey for a one-to-one ortholog and orange where genes share one), 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 color 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 colors, or a dotplot point. Writing color: "grey" lands here. Unset, the default scheme paints.
field
string = ''		field to color each alignment by: strand paints forward and reverse; query and target one color 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 and dnds paint their preset ramps, mapq its bins and syntenicDepth grey for a one-to-one MCScan .anchors or .blocks link and orange where genes share an ortholog; any other name is a column the tracks declare in attributeColumns, a ramp over the values seen for numbers and one color per label for text (or the color a color column put beside it)
scale
maybeStringEnum (none, linear, threshold)		none paints value and keeps the field for a switch back; linear runs a number along a ramp and threshold bins it at the cuts domain lists; unset, a measurement paints its own scale and a column one read off its values
domain
stringArray = []		a text column's labels that take the palette first, in order, and lead the key, the rest following sorted, strand's values (1, -1) in the order range colors them, or a threshold's cuts; a label left out takes a color no listed label or label met before it paints, the first time the view meets it, and keeps it
range
colorArray = []		CSS colors a text column's labels or strand's values 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, dnds or a numeric column), its stops, evenly spaced, in place of the field's own; under threshold, one per interval
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
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
descending
maybeBoolean		threshold key lists the highest interval first; unset follows the field's preset, else the lowest first
title
maybeString		key title; unset keeps the display's own heading, "" draws none