MafColor

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

The MAF display's encoding.color: what fills each species row's aligned cells, as alignments' encoding.color fills its reads. Unset, the theme's match tone fills them, and the X-Y plot's bars take its one bar color. value is a constant fill. identity paints the mean identity to the reference along a ramp, from scale.domainMin 0 to scale.domainMax 1 along the redgreyblue scheme, as every display's identity does. refNameRank paints each block by the rank of its source sequence within the row, rank 0 being the sequence the row aligns most bases from, so a rearranged block stands out. A string is the field. The mismatches and the per-base layer draw over the fill: alignments.mismatches and alignments.bases.

Example usage#

{ type: 'LinearMafDisplay', encoding: { color: 'identity' } }

{
  type: 'LinearMafDisplay',
  encoding: {
    color: { field: 'identity', scale: { domainMin: 0.7, scheme: 'viridis' } },
  },
}

{ type: 'LinearMafDisplay', encoding: { color: { value: '#ccc' } } }

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.

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.

Related links#

• User guide: MAF track