AlignmentsArcColor

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the alignments plugin. View source.

Example usage#

{ type: 'LinearAlignmentsDisplay', readConnections: 'arc', arcColor: 'pairOrientation' }

{
  type: 'LinearAlignmentsDisplay',
  readConnections: 'cloud',
  color: { field: 'insertSize' },
}

See the Config slots section below for all available configuration fields.

The alignments displays' arcColor setting: what colours the read-connection arcs and the read cloud. Empty, the default, the arcs take the reads' color field where it is one an arc paints (insertSize, pairOrientation, insertSizeAndOrientation), and paint insertSizeAndOrientation under any other. A field of its own colours the arcs whatever the reads show. A string is the field.

Config slots#

These slots go on a display entry: "displays": [{ "type": "AlignmentsArcColor", ... }], or in the track's displayDefaults when this is its default display. 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.