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RibbonColor

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the linear-comparative-view plugin. View source.

The multi-way synteny display's ribbons.encoding.color: one color for every ribbon, or a field each ribbon carries: the record's strand (the default, while the channel names neither a field nor a color), a measurement through its preset (identity, mapq, dnds, syntenicDepth), or a column the table declares in attributeColumns, through the same slots as the synteny view's SyntenyColor. A string is the field.

Example usage

{
  type: 'MultiWaySyntenyDisplay',
  ribbons: { encoding: { color: { value: 'rgba(130,130,130,0.3)' } } },
}
{ type: 'MultiWaySyntenyDisplay', ribbons: { encoding: { color: 'strand' } } }
{
  type: 'MultiWaySyntenyDisplay',
  ribbons: {
    encoding: {
      color: {
        field: 'strand',
        scale: {
          range: ['#1b9e77', '#d95f02'],
          names: ['Kept', 'Inverted'],
        },
      },
    },
  },
}
{
  type: 'MultiWaySyntenyDisplay',
  ribbons: {
    encoding: {
      color: {
        field: 'group',
        scale: { domain: ['core', 'shell'], invalid: 'lightgrey' },
      },
    },
  },
}

Config slots

A setting written to it replaces it whole, since its members are alternatives: a member left out returns to its default. 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 ribbon while no field paints.
scale
ConfigurationSchema(
  'RibbonColorScale',
  {
    ...syntenyColorScaleSlots('RibbonColorScaleType'),
    invalid: {
      type: 'maybeColor',
      description:
        'the color of a pair with no value for the field, whose alpha every ribbon takes; unset, rgba(130,130,130,0.3)',
    },
  },
  colorScaleOptions('ribbons.encoding.color.scale'),
)
How the field's values map to colors, Vega-Lite's scale object.
invalid
maybeColor		The color of a pair with no value for the field, Vega-Lite's word for a missing value's output; its alpha is every ribbon's under the field.
legend
ConfigurationSchema(
  'RibbonColorLegend',
  syntenyColorLegendSlots,
  colorLegendOptions,
)
The key this channel draws.
field
string = ''		field to color each ribbon by: strand reads the relative strand between the two lanes the ribbon joins (the two placements' orientations multiplied out, not the drawn twist, so a flipped lane still shows its inversions); identity and dnds paint their preset ramps, mapq its bins and syntenicDepth one-to-one against shared orthologs, as the synteny view's do; any other name is a column the table declares 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)