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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.

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'] },
}
{
  type: 'LinearAlignmentsDisplay',
  color: { field: 'pairOrientation', domain: ['RR'], range: ['#d95f02'] },
}

The alignments displays' color setting: one color for every read, or a field each read carries. A read dimension paints its own vocabulary (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: the facet's own split, spliced, pairing and mateAssembly, a feature attribute, a dotted path into one or a jexl: expression. A string is the constant. The per-base layer over the reads is AlignmentsBaseColor.

Config slots

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, and of a read carrying no value under a tag or attribute, or no mate under mateRefName. Arcs and pair orientations keep the theme's colors. Writing color: "steelblue" lands here. Unset, the theme's read color.
labels
stringArray = []		Names for each level or value range colors, in the same order, in the key, the hovers and the arc key: labels: ["Maternal", "Paternal"] beside domain: ["1", "2"] on tags.HP.
field
string = ''		field to color each read by: strand, firstOfPairStrand, pairOrientation, insertSize, insertSizeAndOrientation and mateRefName paint their own vocabulary and mapq its four bins; tags.XX reads a SAM tag; any other name reads as a facet over it does: split, spliced, pairing, mateAssembly, a feature attribute, a dotted path or a jexl: expression
scale
maybeStringEnum (none, categorical, linear, threshold)		none paints value and keeps the field for a switch back; categorical 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 categorical over any other field
domain
stringArray = []		for a categorical scale, the values that take the range first, in order: a preset field's own 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
domainMin
maybeNumber		the bottom of a linear or log scale's domain; unset follows the loaded values
domainMax
maybeNumber		the top of a linear or log scale's domain; unset follows the loaded values
domainQuantile
number = 1		the quantile an open end of a linear or log scale follows over the loaded values: 1 their extremes, 0.99 clips the outermost 1% at each end, each sign measured on its own
advanced
range
colorArray = []		CSS colors a categorical scale hands its domain in order, or with no domain a preset field's levels in their own order, a threshold scale its bins, or a linear scale's stops, evenly spaced; a level left out keeps its default; empty is the field's own colors, cividis over mapq's bins, the tag palette or viridis
scheme
maybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue, blueyellowred)		a named ramp: a linear or log 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
reverse
boolean = false		turns the ramp round, so its last color paints the bottom of a linear or log domain or a threshold's lowest interval
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
title
maybeString		key title; unset keeps the display's own heading, "" draws none
descending
maybeBoolean		threshold key lists the highest interval first; unset follows the field's preset, else the lowest first