MarkColor
Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the marks plugin. View source.
A mark's encoding.color: one CSS color or jexl: callback for every
instance in value, or a field through scale, Vega-Lite's scale
object: an ordinal scale (a range color per value), a linear, log or
symlog scale (a ramp between domainMin and domainMax, domainMid
placing its middle stop where a diverging ramp turns; symlog runs
logarithmic away from 0 and linear through it, so a signed fold change
ramps on both sides) or a threshold scale (a range color per interval
between the cut points domain lists). A string is the field, as every
channel's is inside encoding; a constant is { value }. legend shapes
the key the scale draws.
Example usage
{ mark: 'bar', encoding: { y: 'score', color: { value: 'steelblue' } } }{ mark: 'point', encoding: { y: 'score', color: 'type' } }{
mark: 'point',
encoding: {
y: 'score',
color: { field: 'strand', scale: { domain: ['1', '-1'] } },
},
}{
mark: 'span',
encoding: {
color: {
field: 'score',
scale: {
type: 'log',
domainMin: 1,
domainMax: 1000,
range: ['white', 'red'],
},
},
},
}{
mark: 'bar',
encoding: {
y: 'score',
color: {
field: 'score',
scale: {
type: 'linear',
domainMin: -2,
domainMax: 6,
domainMid: 0,
range: ['blue', 'white', 'red'],
},
},
},
}{
mark: 'point',
encoding: {
y: 'score',
color: {
field: 'pip',
scale: {
type: 'threshold',
domain: [0.1, 0.5],
range: ['#357ebd', '#eea236', '#d43f3a'],
},
legend: { title: 'PIP', descending: true },
},
},
}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.
| Slot | Description |
|---|---|
valuemaybeColor | A CSS color, or a jexl callback over feature returning one, for a mark whose color is not a scale. Unset, a mark paints in the default blue, #0068d1, and a text mark prints in the page's text color.callback args: feature |
| scale MarkColorScale sub-schema | How the field's values map to colors, Vega-Lite's scale object. |
| legend MarkColorLegend sub-schema | The key this channel's scale draws. |
valuesstringArray = [] | The values an ordinal key lists, in this order; empty lists every value the loaded regions met. A value left out still paints, as Vega-Lite's legend.values and ggplot2's breaks leave it. |
missingLabelmaybeString | The key's name for a feature with nothing in field; unset is "(no value)". Vega-Lite's legend has no such member, so it keeps its JBrowse name. |
fieldfeatureField = '' | the feature field a scale reads, or a jexl expression over feature, which is slower per feature and so the opt-in |
scale.typemaybeStringEnum (ordinal, linear, log, symlog, threshold) | ordinal hands out range colors per distinct value; linear, log and symlog read the value between domainMin and domainMax into a ramp; threshold cuts the value at the domain and hands each interval a range color; unset is linear for score and ordinal for any other field |
scale.domainstringArray = [] | for an ordinal scale, the values in legend order, walking the range from the first entry and continuing into the default palette past its end (a value left out takes a color no listed value or value met before it paints, the first time the track shows it, and keeps it); for a threshold scale, the cut points in ascending order, a value taking the range entry for the number of them it is at or past, so range has one entry more than this; a linear or log scale reads domainMin and domainMax instead |
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 |
scale.rangecolorArray = [] | CSS colors an ordinal scale hands its domain in order, a threshold scale its intervals, or a ramp's evenly spaced stops; empty is the default palette, or the scheme |
scale.unknownmaybeColor | color for a value missing from domain: unset takes the next palette color where the display deals one, a color paints that color, "" adds no color from this setting, so a row keeps the color it already has, a variant cell takes the alt hue and a feature the no-value grey |
scale.invalidmaybeColor | color for a feature with no value under an ordinal scale's field; unset, the display's no-value color |
scale.namesstringArray = [] | key name for each domain value, one each in order, or under threshold for each interval from the lowest; a value past the end of the list shows its own |
scale.schememaybeStringEnum (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.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 |
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 |
Related links
- Config guide: GWAS track