ScoreFieldConfigMixin
Auto-generated @jbrowse/mobx-state-tree API for the current JBrowse release — see pluggable elements for concepts. Built into JBrowse core. View source.
WiggleScoreConfigMixin plus scoreField, for a display that plots one
configured feature field and so declares scoreFieldConfigSchemaFields:
the wiggle display. LinearMarkDisplay names a field per mark and composes
the base instead.
Members a composed model contributes are listed here too, so these tables are the whole surface.
Volatiles
| Member | Description | Defined by |
|---|---|---|
unclippedQuantileunclippedQuantile: undefined as number | undefined | ScoreScaleMixin |
Getters
| Member | Description | Defined by |
|---|---|---|
scoreFieldstring | The feature field the worker plots on the score axis, score by default. A fetch input: every composing display carries it in its rpcProps(), since the field is read where the features are. | ScoreFieldConfigMixin |
sizenumber | WiggleScoreConfigMixin | |
isDensityModeboolean | Whether score maps to color instead of height; a display overrides it. | WiggleScoreConfigMixin |
axisReachesZeroboolean | A density row maps score to colour and has no axis to start at 0, so its domain spans the values whatever scales.y.zero says. | WiggleScoreConfigMixin |
scaleTypestring | ScoreScaleMixin | |
scaleZeroboolean | scales.y.zero: whether an autoscaled linear or symlog axis reaches 0. | ScoreScaleMixin |
domainQuantilenumber | scales.y.domainQuantile: what an unpinned end follows, 1 the extremes and below it that quantile of each sign. | ScoreScaleMixin |
clipQuantilenumber | 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. | ScoreScaleMixin |
symlogConstantnumber | Raw slot; 0 means "derive from the domain". Resolve it with resolveSymlogConstant once the domain is known. | ScoreScaleMixin |
manualMinScorenumber | undefined | The lower bound the config pins, undefined where it pins none. | ScoreScaleMixin |
manualMaxScorenumber | undefined | The upper bound the config pins, undefined where it pins none. | ScoreScaleMixin |
valueScaleNoticesstring[] | What scales.y's ends say together that the axis cannot draw as written, as corner-notice lines, by the rule a colour ramp's ends answer to. The mark display reports them through its rule list. | ScoreScaleMixin |
autoscaleGroupstring | undefined | scales.y.autoscaleGroup, undefined while it names none. | ScoreScaleMixin |
scaleTitlestring | scales.y.title, '' while unset | ScoreScaleMixin |
gridboolean | scales.y.grid | ScoreScaleMixin |
minimalTicksboolean | scales.y.minimalTicks | ScoreScaleMixin |
scoreRulesDrawnboolean | 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 colour-mapped rows and a colour ramp do not. | ScoreScaleMixin |
scoreRulesValueScaleRule[] | scales.y.rules, read off the live nodes: a snapshot strips a slot at its default, and a rule at 0 is one. | ScoreScaleMixin |
defaultScoreDomain[number | undefined, number | undefined] | Overridable hook: what each end of the domain falls back to where the config leaves its bound unset. [undefined, undefined] — the default — means autoscale both ends, which is right for a track whose scores have no absolute meaning (a bigwig's units are its own).A display whose scores are bounded by construction overrides it, so the axis stops being a function of what happens to be on screen: GC content is a fraction, so 0 and 1 are its real limits and mean the same thing at every locus. Autoscaled, the same GC value drew at different heights depending on where the user had panned, and the track could not be read across loci. A hook rather than a config default because the answer can depend on the data — the wiggle display reads the bounds its adapter declares, a GC content track's [0, 1] — and rather than each display re-resolving the sentinels, which is the one thing that must not be duplicated: config bounds still win, precisely because they are checked before this is consulted. | ScoreAxisMixin |
valueScalesValueScale[] | Overridable hook (default none): the scales this display draws its y through. A display that answers it gets an axis per band of each, with its cross-hatches, placed by DisplayChrome and renderDisplaySvg, and the ticks derived below. | ScoreAxisMixin |
autoscaleRange[number, number] | undefined | Overridable: what this display's own data spans, before any bound, nice-rounding or group widens it; what a group unions. | ScoreAxisMixin |
autoscaledDomain[number, number] | undefined | The domain an autoscaled axis draws: autoscaleRange, widened to every range its autoscaleGroup holds, nice-rounded inside this display's own bounds. Each member unions the others' own ranges and never their domains, so a pinned end stays the display's that pinned it. undefined while this display has nothing of its own to scale. | ScoreAxisMixin |
minScoreBoundnumber | undefined | Resolved lower bound; undefined means autoscale this end. | ScoreAxisMixin |
maxScoreBoundnumber | undefined | Resolved upper bound; undefined means autoscale this end. | ScoreAxisMixin |
hasManualScoreBoundsboolean | Whether the user has pinned either end, which is a different question from whether either end resolved to a number: defaultScoreDomain fills the unset ends in, so a GC content track answers yes to the second with nothing configured. The score menu asks this one — it captions the min/max row with the range in force, and a caption off the resolved pair named a range on every freshly opened GC content track. | ScoreAxisMixin |
axesYAxis[] | The axes, one per declared scale whose domain resolved: where each tick lands in the band's own pixel space, through computeYTicks unless the scale brought its own ladder, and where each of the scale's rules inside the domain lands in that same box, through the scale type the renderer places its values by. | ScoreAxisMixin |
Actions
| Member | Description | Defined by |
|---|---|---|
setSize(val?: number | undefined) => void | WiggleScoreConfigMixin | |
setScaleType(scaleType: string) => void | ScoreScaleMixin | |
setScaleZero(zero: boolean) => void | ScoreScaleMixin | |
setDomainQuantile(quantile: number) => void | ScoreScaleMixin | |
setMinScore(val?: number | undefined) => void | ScoreScaleMixin | |
setMaxScore(val?: number | undefined) => void | ScoreScaleMixin | |
setAutoscaleGroup(group?: string | undefined) => void | ScoreScaleMixin | |
setGrid(grid: boolean) => void | ScoreScaleMixin | |
setScoreRules(rules: (number | ValueScaleRule)[]) => void | Replaces scales.y.rules whole, each entry in a form the config takes: a number, or { value, color, label }. | ScoreScaleMixin |