AlignmentsColor

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', color: { field: 'strand' } }

{
  type: 'LinearAlignmentsDisplay',
  color: { field: 'tags.HP', domain: ['1', '2'], range: ['#d95f02', '#1b9e77'] },
}

{
  type: 'LinearAlignmentsDisplay',
  color: { field: 'tags.NM', scale: 'linear', scheme: 'viridis' },
}

{
  type: 'LinearAlignmentsDisplay',
  color: { field: 'insertSize', domain: ['150', '600'] },
}

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

The alignments displays' color setting: one colour for every read, or a field each read carries. A read dimension paints its own vocabulary (strand, firstOfPairStrand, pairOrientation, insertSize, insertSizeAndOrientation, mateRefName) or ramp (mapq), tags.XX reads a SAM tag and any other name a feature attribute. A string is the constant. The per-base layer over the reads is AlignmentsBaseColor.

Related links#

• Extended by: LGVSyntenyColor

Config slots#

These slots go on a display entry: "displays": [{ "type": "AlignmentsColor", ... }], 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.