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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 read dimension colors by its fixed levels (strand, firstOfPairStrand, pairOrientation, insertSize, insertSizeAndOrientation, mateRefName) or bins (mapq, the four a facet over it stacks), 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. split, spliced, pairing and svSignal color nothing: reads keep their arcs' colors, and a facet sections them by those. 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',
  encoding: { color: { field: 'insertSize', scale: { domain: [150, 600] } } },
}
{
  type: 'LinearAlignmentsDisplay',
  encoding: {
    color: {
      field: 'pairOrientation',
      scale: { domain: ['RR'], range: ['#d95f02'] },
    },
  },
}

Config slots

A setting written to it replaces it whole, since its members are alternatives: 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.

SlotDescription
value
maybeColor		The fill of every read while no field paints. Arcs and pair orientations keep the theme's colors. Unset, the theme's read color.
scale
AlignmentsColorScale sub-schema		How the field's values map to colors, Vega-Lite's scale object.
invalid
maybeColor		The fill of a read with no value under the field, Vega-Lite's word for a missing value's output: no tag, no attribute, or no mate under mateRefName. A '' in domain colors it by its range entry instead.
unknown
maybeColor		The fill of a read whose tag, attribute, mate reference or MAPQ an ordinal domain leaves out, d3's ordinal.unknown: unknown: "#999" beside domain: ["1", "2"] on tags.HP paints every other haplotype grey, and the key lists them as one row, Other. A field with fixed levels, such as strand, has no value outside them.
names
stringArray = []		Names for each level or value range colors, in the same order, in the key, the hovers and the arc key: names: ["Maternal", "Paternal"] beside domain: ["1", "2"] on tags.HP.
legend
AlignmentsColorLegend sub-schema		The key this channel draws.
field
string = ''		field to color each read by: strand, firstOfPairStrand, pairOrientation, insertSize, insertSizeAndOrientation and mateRefName color by their fixed levels and mapq by its four bins; tags.XX reads a SAM tag; any other name reads as a facet over it does: mateAssembly, a feature attribute, a dotted path or a jexl: expression; split, spliced, pairing and svSignal color nothing, as a facet sections by them
scale.type
maybeStringEnum (ordinal, linear, threshold)		ordinal a range color per value; linear a ramp over mapq or a numeric tag or attribute between domainMin and domainMax; threshold the bins domain cuts; unset, threshold over insertSize, insertSizeAndOrientation and mapq, and ordinal over any other field
scale.domain
stringArray = []		for an ordinal scale, the values that take the range first, in order: a preset field's levels (strand 1 and -1; pairOrientation LR, RL, RR and LL; insertSize short, normal and long; under the insert-size and orientation fields, unmappedMate and interchrom, and in a chain under the orientation ones splitInverted, splitSameStrand, segmentInverted and segmentSameStrand; '' a read with no value), a MAPQ, 255 for unavailable, or a tag's values; for a threshold scale, the cut points, which over insertSize are the two between short, normal and long, where the sampled distribution otherwise sets them, and over mapq 1, 10 and 30
scale.range
colorArray = []		CSS colors an ordinal scale hands its domain in order, or with no domain a preset field's levels in their preset order, a threshold scale its bins, or a linear scale's stops, evenly spaced; a level left out keeps its default; empty uses the field's default colors, cividis over mapq's bins, the tag palette or viridis
scale.scheme
maybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue, redyellowblue)		a named ramp: a linear, log or symlog scale runs along it, and a threshold that writes cuts takes one color per interval from end to end; range's colors, where it lists any, win over it
scale.reverse
maybeBoolean		turns the ramp round, so its last color paints the bottom of a ramp's domain or a threshold's lowest interval; unset follows the field's preset, else runs as written
scale.domainMid
maybeNumber		the value the ramp's middle stop sits at, so a diverging ramp centres somewhere other than the middle of the domain, both sides on one scale: the farther end of the domain reaches its end color and equal distances from the middle take equal colors; unset, the stops are evenly spaced across it
scale.domainMin
maybeNumber		the bottom of a ramp's domain; unset follows the loaded values
scale.domainMax
maybeNumber		the top of a ramp's domain; unset follows the loaded values
scale.domainQuantile
number = 1		the quantile an open end of a ramp follows over the loaded values: 1 their extremes, 0.99 clips the outermost 1% at each end, each sign measured on its own
advanced
legend.title
maybeString		key title; unset keeps the display's own heading, "" draws none
legend.descending
maybeBoolean		threshold key lists the highest interval first; unset follows the field's preset, else the lowest first