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YFieldChannel

Auto-generated from the config schema in the source — see the config guide for concepts. Built into JBrowse core. View source.

A YChannel that also names the field it plots, the wiggle display's encoding.y. A bare string is the field.

Example usage

The bins' maxima on a log axis:

{
  type: 'LinearWiggleDisplay',
  encoding: { y: { field: 'maxScore', scale: { type: 'log' } } },
}

The whole visible range, spikes included, rather than the fence the wiggle display starts on:

{
  type: 'LinearWiggleDisplay',
  encoding: { y: { scale: { fenceQuantile: 1 } } },
}

Config slots

A setting written to it names members one by one: a member left out stays as it is, and null resets one. 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
featureField = 'score'		the feature field plotted on the value axis, as a mark's encoding.y names one. score, minScore and maxScore are a zoom bin's stored mean, minimum and maximum, which every quantitative source serves, a raw record answering its score for all three. Any other name, a dotted path or a jexl: expression reads a raw column the adapter left alone (a BED extra column, a GFF attribute) and draws no min-max extent. A feature with no finite value in the field plots at 0
Inherited from YChannel6 slots
rules.value
number = 0		The rule's position on the axis, in the units the axis plots: a -log10(p) over a Manhattan plot, a depth over coverage.
rules.color
maybeColor		The line's color, and its label's. Unset draws every rule in the one color the chrome rules plots in, so a threshold that means something particular — genome-wide significance, a diploid depth — is one an author paints, on the plot where it means it.
rules.label
string = ''		Free text drawn at the rule's right-hand end. JBrowse assigns it no meaning: "2 copies" over a coverage plot is a claim only the author can make, since no ploidy can be assumed.
scale
YScale		type, domainMin, domainMax, zero, fenceQuantile, constant and group.
axis
YAxis		title and grid.
rules
list of ValueScaleRule entries		Horizontal reference lines, each { value, color, label } or a bare number. An autoscaled end widens to keep every rule on the axis; a pinned end that excludes one drops it.