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ValueScale

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

Example usage

A log axis floored at 1:

{
  type: 'LinearWiggleDisplay',
  scales: { y: { type: 'log', domainMin: 1 } },
}

The whole visible range, rather than the 99th percentile the wiggle displays start on:

{
  type: 'LinearWiggleDisplay',
  scales: { y: { autoscale: 'local' } },
}

A titled axis with a labelled genome-wide threshold over a plain suggestive one:

{
  type: 'LinearMarkDisplay',
  scales: {
    y: {
      title: '-log10 p',
      rules: [{ value: 7.3, color: 'red', label: 'p = 5e-8' }, 5],
    },
  },
}

See the Config slots section below for all available configuration fields.

The value scale of a quantitative display, written as scales.y: the wiggle and multi-wiggle plots, the Manhattan plot, the alignments coverage band and the mark display each carry one. Which members it has follows what the display draws: Manhattan places a linear axis and consults no autoscale mode, so it has neither type alternatives nor autoscale.

Vega-Lite's spelling: a pinned end is domainMin or domainMax, and an end left unset autoscales over the loaded regions.

Two defaults come from the display rather than from the scale. autoscale starts at localpercentile on the wiggle and multi-wiggle plots and at local on the coverage band and the mark display. symlogConstant starts at 0 on the wiggle family and at 1 on the coverage band.

The wiggle family, the Manhattan plot and the mark display also carry rules, reference lines at chosen values; the mark display adds title, the caption beside the axis. A rule naming no color draws in the one colour the chrome rules every plot in, so a red line is a claim its author makes rather than a meaning a display assigns.

Config slots

These slots go on a display entry: "displays": [{ "type": "ValueScale", ... }], 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
scales.y.rules.value
number = 0		Where the rule sits on the axis, in the units the axis plots: a -log10(p) over a Manhattan plot, a depth over coverage.
scales.y.rules.color
maybeColor		The line's colour, and its label's. Unset draws every rule in the one colour 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.
scales.y.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.
scales.y.type
stringEnum = 'linear'		How the axis reads its domain — the ticks, the cross-hatches and the renderer's placement all come from it. log cannot represent 0 or negative values and floors the domain above them; symlog is log-like away from zero and linear through it, so a track whose values touch or cross 0 keeps them. Which of the three a display offers is which of them its renderer places.
scales.y.domainMin
maybeNumber		The bottom of the axis, pinning what would otherwise autoscale to the loaded regions. Unset autoscales that end. The score menu's "Set min/max" writes here.
scales.y.domainMax
maybeNumber		The top of the axis. Unset autoscales that end.
scales.y.symlogConstant
number = per display		Width of symlog's linear region around zero. 0 derives it from the domain, a thousandth of its largest magnitude — right for a wiggle track, whose units are its own. The coverage band starts at 1 instead, which makes symlog exactly log(depth+1) and puts the knee at one read.
advanced
scales.y.autoscale
stringEnum = per display		What an unpinned end scales to: local takes the extremes of the visible region, localsd the mean ± numStdDev standard deviations, localpercentile the numQuantile-th percentile of each sign, which is robust to a peaky distribution.
scales.y.numStdDev
number = 3		Standard deviations either side of the mean the localsd autoscale reaches.
advanced
scales.y.numQuantile
number = 0.99		The percentile localpercentile clips outliers at — 0.99 drops the outermost 1% of each sign. The two signs are measured independently and anchored at 0, so a sparse minority tail stays visible and all-positive data pins its bottom at 0.
advanced
scales.y.title
maybeString		The caption beside the axis, naming what it measures, drawn once however many bands the scale rules. Three states: unset, the display derives it (the mark display from the encoding.y field every mark drawing a value at the view's zoom shares, and none where they differ or one is a jexl: expression); some text is that text; "" is an axis with no caption, and the only spelling of one. null reads as unset, as it does in every slot, so it derives the caption — where Vega-Lite and GenomeSpy read title: null as no title.
scales.y.rules
types.array(valueScaleRuleSchema())		Horizontal reference lines at chosen values, across every band the scale rules: a significance threshold, a zero line, an allele-frequency cut. Each is { value, color, label }, or a bare number for a plain line. An autoscaled end widens to keep every rule on the axis; a pinned domainMin or domainMax that excludes a rule drops it.