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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.

The linear synteny, dotplot and circular views' encoding.color, which every track in the view paints with: one color for every alignment, or a field of each alignment — 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 ramp for numbers and a color per label once a value is text, unless scale.type says otherwise (ordinal paints integer group ids a color each). A string is the field.

Example usage

{ type: 'LinearSyntenyView', encoding: { color: 'strand' } }
{ type: 'DotplotView', encoding: { color: { field: 'query' } } }
{
  type: 'LinearSyntenyView',
  encoding: {
    color: { field: 'identity', scale: { scheme: 'magma', domainMin: 0.9 } },
  },
}
{
  type: 'LinearSyntenyView',
  encoding: {
    color: {
      field: 'identity',
      scale: { type: 'threshold', domain: [0.95, 0.99] },
    },
  },
}
{
  type: 'LinearSyntenyView',
  encoding: {
    color: {
      field: 'gene_group',
      scale: {
        domain: ['A1a', 'B1'],
        range: ['#1b9e77', '#d95f02'],
        names: ['Subgenome A', 'Subgenome B'],
      },
      legend: { title: 'Gene group' },
    },
  },
}

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 while no field paints, 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. Unset, the default scheme paints.
scale
SyntenyColorScale sub-schema		How the field's values map to colors, Vega-Lite's scale object.
legend
SyntenyColorLegend sub-schema		The key this channel draws.
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.type
maybeStringEnum (linear, threshold, ordinal)		linear runs a number along a ramp, threshold bins it at the cuts domain lists, and ordinal paints a column's values one color each, numbers included (a measurement keeps its preset); a written type wins over the values, so a text value under linear or threshold paints as missing; unset, a measurement uses its preset scale and a column linear for numbers and ordinal once a value is text
scale.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
scale.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 default stops; under threshold, one per interval
scale.scheme
maybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue, redyellowblue)		a named ramp: a ramp scale runs along it, a threshold that writes cuts takes one color per interval from end to end, and an ordinal scale that lists a domain one per value; range's colors, where it lists any, win over it
scale.reverse
maybeBoolean		turns the ramp round, so its last color paints the bottom of a ramp's domain or a threshold's lowest interval; unset follows the field's preset, else runs as written
scale.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
scale.domainMin
maybeNumber		the bottom of a ramp's domain; unset follows the loaded values
scale.domainMax
maybeNumber		the top of a ramp's domain; unset follows the loaded values
scale.names
stringArray = []		key name for each domain value, one each in order, or under threshold for each interval from the lowest; a value past the end of the list shows its own
scale.unknown
maybeColor		color for a value missing from domain. Unset: the next palette color where the display deals one, and the levels a preset field names, such as strand's, keep their own colors. A color: that color. "": no color dealt, so a feature paints the no-value grey, a variant cell the alt hue, and a row keeps the color it already has
scale.invalid
maybeColor		color for a feature with no value under an ordinal scale's field; unset, the display's no-value color
legend.title
maybeString		key title; unset keeps the display's own heading, "" draws none
legend.descending
maybeBoolean		threshold key lists the highest interval first; unset follows the field's preset, else the lowest first