AlignmentsColor

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

The alignments displays' encoding.color: one color for every read in value, or a field of each read. A preset field, listed below, colors by its levels or bins, tags.XX reads a SAM tag, and any other name reads the read as a facet over it does: mateAssembly, a feature attribute, a dotted path into one or a jexl: expression. A string is the field. Unlike a feature track, which deals colors in the order values appear, a tag or attribute with no scale.domain, range or unknown colors each value by its text alone, so the value keeps its color in every region and session. split, spliced, pairing, svKind and svSignal color nothing: reads keep their arcs' colors. A facet sections them by the first four, and the svSignal filter keeps or hides SV evidence. The per-base layer over the reads is pileup.bases.

Example usage#

{ type: 'LinearAlignmentsDisplay', encoding: { color: 'strand' } }

{
  type: 'LinearAlignmentsDisplay',
  encoding: {
    color: {
      field: 'tags.HP',
      scale: {
        domain: ['1', '2'],
        range: ['#d95f02', '#1b9e77'],
        names: ['Maternal', 'Paternal'],
        invalid: '#cccccc',
      },
    },
  },
}

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

{
  type: 'LinearAlignmentsDisplay',
  normalInsertSize: { min: 150, max: 600 },
  encoding: {
    color: {
      field: 'insertSizeAndOrientation',
      scale: { domain: ['RR'], range: ['#d95f02'] },
    },
  },
}

Related links#

• Extended by: LGVSyntenyColor

Preset fields#

A field named here paints through its own scale while scale.type is unset, and range and names index its levels in order while domain is unwritten. Any other field is ordinal.

Config slots#

A setting written to it replaces it whole: 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.