# ValueScale
Auto-generated config schema for the current JBrowse release — see the [config guide](https://jbrowse.org/jb2/docs/config_guide) for concepts. Built into JBrowse core. [View source](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/valueScaleConfigSchema.ts).
## Example usage
A log axis floored at 1:
```js
{
type: 'LinearWiggleDisplay',
scales: { y: { type: 'log', domainMin: 1 } },
}
```
The whole visible range, rather than the 99th percentile the wiggle
displays start on:
```js
{
type: 'LinearWiggleDisplay',
scales: { y: { autoscale: 'local' } },
}
```
A titled axis with a labelled genome-wide threshold over a plain
suggestive one:
```js
{
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`](https://jbrowse.org/jb2/docs/config_guides/tracks#configuring-displays) when this is its default display. Slot types (`fileLocation`, `frozen`, ...) are explained in the [config slot types reference](https://jbrowse.org/jb2/docs/config_guides/slot_types). Slots a base configuration contributes are listed here too, so this table is the whole surface.
| Slot | Description |
| --- | --- |
| **scales.y.rules.value**
[`number`](https://jbrowse.org/jb2/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2/docs/config_guides/slot_types#the-maybe-types) | 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`](https://jbrowse.org/jb2/docs/config_guides/slot_types#the-maybe-types) | The top of the axis. Unset autoscales that end. |
| **scales.y.symlogConstant**
[`number`](https://jbrowse.org/jb2/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2/docs/config_guides/slot_types#number) = 3 | Standard deviations either side of the mean the `localsd` autoscale reaches.
_advanced_ |
| **scales.y.numQuantile**
[`number`](https://jbrowse.org/jb2/docs/config_guides/slot_types#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`](https://jbrowse.org/jb2/docs/config_guides/slot_types#the-maybe-types) | 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. |