Skip to main content

ScoreScaleMixin

Auto-generated from the @jbrowse/mobx-state-tree model in the source — see the developer guide for concepts. Built into JBrowse core. View source.

Value scale, written in scales.y. valueScaleSchema / scalesSchema. Brings ScoreAxisMixin plus scaleType / scaleZero / domainQuantile / clipQuantile / symlogConstant / manual* and their setters, i.e. the whole ScoreScaleModel interface the Y axis row and its drawer widget consume

The value scale of every quantitative display: wiggle, the alignments coverage band and the mark display, Manhattan among them, each declare scales.y through valueScaleSchema and compose this. It backs ScoreAxisMixin's three overridable members off that object and adds the setters that write it, so composing this is how a display satisfies ScoreScaleModel in scoreMenuItems.ts — the interface the Y axis row and its drawer widget consume.

Deliberately just the scale and the guides it owns. Colors, resolution and the autoscale computation stay in WiggleScoreConfigMixin / WiggleCommonMixin — the alignments coverage band shares this scale but none of the rest.

Each section ends with the members a composed model contributes, linked to the page that documents them.

Volatiles

MemberDescription
unclippedQuantile
number | undefined

Getters

MemberDescription
scaleType
string
scaleZero
boolean		scales.y.zero: whether an autoscaled linear or symlog axis reaches 0.
domainQuantile
number		scales.y.domainQuantile: what an unpinned end follows, 1 the extremes and below it that quantile of each sign.
clipQuantile
number		The quantile "Clip extreme outliers" fences at: the one an untick this session wrote over, else the scale's own default where that is below 1, else 0.99.
symlogConstant
number		Raw slot; 0 means "derive from the domain". Resolve it with resolveSymlogConstant once the domain is known.
manualMinScore
number | undefined		The lower bound the config pins, undefined where it pins none.
manualMaxScore
number | undefined		The upper bound the config pins, undefined where it pins none.
valueScaleNotices
string[]		What scales.y's ends say together that the axis cannot draw as written, as corner-notice lines, by the rule a color ramp's ends answer to. The mark display reports them through its rule list.
autoscaleGroup
string | undefined		scales.y.autoscaleGroup, undefined while it names none.
scaleTitle
string		scales.y.title, '' while unset
grid
boolean		scales.y.grid
minimalTicks
boolean		scales.y.minimalTicks
scoreRulesDrawn
boolean		Whether this display draws scales.y.rules, which is whether the Y axis panel offers Include 0 and the reference lines: a scale it places y through rules a band for them to cross, which a density plot's color-mapped rows and a color ramp do not.
scoreRules
ValueScaleRule[]		scales.y.rules, read off the live nodes: a snapshot strips a slot at its default, and a rule at 0 is one.
9 inherited getters from one model

From ScoreAxisMixin: defaultScoreDomain, valueScales, autoscaleRange, axisReachesZero, autoscaledDomain, minScoreBound, maxScoreBound, hasManualScoreBounds, axes

Actions

MemberDescription
setScaleType
(scaleType: string) => void
setScaleZero
(zero: boolean) => void
setDomainQuantile
(quantile: number) => void
setMinScore
(val?: number | undefined) => void
setMaxScore
(val?: number | undefined) => void
setAutoscaleGroup
(group?: string | undefined) => void
setGrid
(grid: boolean) => void
setScoreRules
(rules: (number | ValueScaleRule)[]) => void		Replaces scales.y.rules whole, each entry in a form the config takes: a number, or { value, color, label }.