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SyntenyOpacity

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

The synteny views' encoding.opacity, as encoding.color is their color: one opacity for every alignment, or a field of each alignment read into opacities. A number is the constant and is written to value; a string is the field and is written to field. Under a field, scale.range holds the opacities themselves, so a field that fades a dense view keeps it dim by writing a low range.

Example usage

{ type: 'LinearSyntenyView', encoding: { opacity: 0.3 } }
{
  type: 'LinearSyntenyView',
  encoding: { opacity: { field: 'identity', scale: { range: [0.1, 0.6] } } },
}
{
  type: 'LinearSyntenyView',
  encoding: {
    opacity: {
      field: 'break_FET',
      scale: { type: 'threshold', domain: [0.05], range: [0.8, 0.15] },
    },
  },
}

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
maybeNumber		The opacity of every alignment, 0 to 1, while no field fades them. Unset is the view's own default. Writing opacity: 0.3 lands here.
field
string = ''		The field that fades each alignment: a measurement (identity, mapq, dnds) or a column the tracks declare in attributeColumns. Empty draws every alignment at value. Writing opacity: "identity" sets it.
scale
SyntenyOpacityScale sub-schema		How the field's values map to opacities.
scale.type
maybeStringEnum (threshold)		threshold reads domain as cut points, a value on a cut taking the interval above it. Unset, a number column fades linearly from domainMin to domainMax and a text column takes one opacity per label.
scale.domain
stringArray = []		A text column's labels, which take range in order; under threshold, the cut points.
scale.range
stringArray = []		The opacities, 0 to 1: a number column's at domainMin and domainMax, a text column's per domain label, a threshold's per interval, one more than the cuts. Empty fades a number column from 0.3 to 1; a label or interval past the list draws opaque.
scale.domainMin
maybeNumber		The value a number column is faintest at; unset, the measurement's own floor or the least value seen.
scale.domainMax
maybeNumber		The value a number column is most opaque at; unset, the measurement's own ceiling or the greatest value seen.