Skip to main content

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.

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.

SlotDescription
field
string = 'strand'		strand, mapq and mateRefName (the query contig) are the fields a synteny block answers.
Inherited from AlignmentsColor9 slots
value
maybeColor		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.
scale
maybeStringEnum (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
domain
stringArray = []		for a categorical scale, the values that take the range first, in order; 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
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
range
colorArray = []		CSS colours a categorical scale hands its domain in order, a threshold scale its bins, or a linear scale's stops, evenly spaced; empty is the tag palette or viridis
scheme
maybeStringEnum (viridis)		a named ramp for a linear or log scale; range's colours, where it lists any, win over it
reverse
boolean = false		turns a linear or log scale's ramp round, so its last colour paints the bottom of the domain
domainMid
maybeNumber		the value the ramp's middle stop sits at, so a diverging ramp centres somewhere other than the middle of the domain; unset, the stops are evenly spaced across it