LGVSyntenyColor
Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the linear-comparative-view plugin. View source.
The LGVSyntenyDisplay's encoding.color: the
AlignmentsColor channel, painting strand while it
names neither a field nor a constant. strand, mapq and mateRefName
(the query contig) are the fields a synteny block answers.
Example usage
{ type: 'LGVSyntenyDisplay', encoding: { color: 'mateRefName' } }Related links
- Base config: AlignmentsColor
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.
| Field | Scale | Levels | Names | Other defaults |
|---|---|---|---|---|
strand | ordinal | 1, -1 | ||
mapq | threshold | 1, 10, 30 | MAPQ 0 (multi-mapping), MAPQ 1-9 (low), MAPQ 10-29, MAPQ 30+ (high confidence) | scheme: cividis; key "Mapping quality" |
firstOfPairStrand | ordinal | 1, -1 | ||
insertSizeAndOrientation | ordinal | short, normal, long, RL, RR, LL, mateUnmapped, interchrom, splitInverted, splitSameStrand, unpairedSplitInverted, unpairedSplitSameStrand | ||
mateRefName | 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.
| Slot | Description |
|---|---|
| Inherited from AlignmentsColor | 18 slots |
valuemaybeColor | 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. |
scale.invalidmaybeColor | 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. |
scale.unknownmaybeColor | 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. |
scale.namesstringArray = [] | 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. |
fieldstring = '' | field to color each read by: a preset field by its levels or 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, svKind and svSignal color nothing: a facet sections by the first four and the svSignal filter keeps or hides SV evidence |
scale.typemaybeStringEnum (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 mapq and ordinal over any other field |
scale.domainstringArray = [] | for an ordinal scale, the values that take the range first, in order: a preset field's levels, insertSizeAndOrientation's short, normal, long and RL among them, '' a read with no value, a MAPQ, 255 for unavailable, or a tag's values; for a threshold scale, the cut points; the display's normalInsertSize sets the insert sizes between short and long |
scale.rangecolorArray = [] | 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.schememaybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue, redyellowblue) | a named ramp: a ramp scale runs along it, a threshold that writes cuts takes one color per interval from end to end, and an ordinal scale that lists a domain one per value; range's colors, where it lists any, win over it |
scale.reversemaybeBoolean | 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.domainMidmaybeNumber | 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.domainMinmaybeNumber | the bottom of a ramp's domain; unset follows the loaded values |
scale.domainMaxmaybeNumber | the top of a ramp's domain; unset follows the loaded values |
scale.domainQuantilenumber = 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.titlemaybeString | key title; unset keeps the display's own heading, "" draws none |
legend.descendingmaybeBoolean | threshold key lists the highest interval first; unset follows the field's preset, else the lowest first |