LGVSyntenyColor
Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the linear-comparative-view plugin. View source.
Example usage
{ type: 'LGVSyntenyDisplay', color: { field: 'mateRefName' } }See the Config slots section below for all available configuration fields.
The LGVSyntenyDisplay's color setting: the
AlignmentsColor object with field defaulting to
strand, where the alignments display paints one fill. A string is the
constant, { value, scale: 'none' }, so the default field does not hide it.
Related links
- Base config: AlignmentsColor
Config slots
These slots go on a display entry: "displays": [{ "type": "LGVSyntenyColor", ... }], or in the track's displayDefaults when this is its default display. 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 |
|---|---|
fieldstring = 'strand' | strand, mapq and mateRefName (the query contig) are the fields a synteny block answers. |
| Inherited from AlignmentsColor | 10 slots |
valuemaybeColor | The fill of every read while no field paints, and of a read carrying no value under a tag or attribute. Writing color: "steelblue" lands here. Unset, the theme's read colour. |
scalemaybeStringEnum (none, categorical, linear, threshold) | none paints value and keeps the field for a switch back; categorical a range colour per value; linear a ramp over a numeric tag or attribute between domainMin and domainMax; threshold the bins domain cuts; unset, threshold over insertSize and insertSizeAndOrientation and categorical over any other field |
domainstringArray = [] | 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; mapq 255 for unavailable; '' a read with no value) 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 |
domainMinmaybeNumber | the bottom of a linear or log scale's domain; unset follows the loaded values |
domainMaxmaybeNumber | the top of a linear or log scale's domain; unset follows the loaded values |
domainQuantilenumber = 1 | the quantile an open end of a linear or log scale follows over the loaded values, each sign anchored at 0: 1 their extremes, 0.99 clips the outermost 1% advanced |
rangecolorArray = [] | CSS colours 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 colours, the tag palette or viridis |
schememaybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange) | a named ramp for a linear or log scale; range's colours, where it lists any, win over it |
reverseboolean = false | turns a linear or log scale's ramp round, so its last colour paints the bottom of the domain |
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 colour and equal distances from the middle take equal colours; unset, the stops are evenly spaced across it |