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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 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
ConfigurationSchema(
  'SyntenyColorScale',
  syntenyColorScaleSlots('SyntenyColorScaleType'),
  colorScaleOptions('encoding.color.scale'),
)
How the field's values map to colors, Vega-Lite's scale object.
legend
ConfigurationSchema(
  'SyntenyColorLegend',
  syntenyColorLegendSlots,
  colorLegendOptions,
)
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)