OptionaltitleOverrides the layer's announced title. Maps to MaidrLayer.title.
Names the chart; use DeclarationBase.name to say which layer of it this is.
OptionalnameNames this layer among sibling layers. Maps to MaidrLayer.name.
Announced on a layer switch in place of the trace type, so a hue-split figure says "Male" and "Female" rather than "error_bar plot" twice.
OptionallabelField holding what each point is — a SNP id, a probe, a marker. Maps to
VolcanoPoint.label.
Identity is the payload on these charts, not the coordinates: a reader told "x is 2.3, y is 14.1" has been given the two numbers whose shape they can already hear and withheld the one thing they came for. Left out of the payload when nothing resolves.
OptionalgroupField holding the region a point belongs to — its chromosome. Maps to
VolcanoPoint.group.
OptionalsignificanceThe significance cutoff on the y axis, on the axis the chart is drawn
against — 7.3 for genome-wide significance on a -log10(p) axis. Maps to
MaidrLayer.thresholdOptions.significance.
There is deliberately no default: the conventions differ by field and by software, and a guessed line would sort every point on the figure onto the wrong side, silently. Undeclared, the trace simply reports no findings.
OptionalsignificanceWhich side of significance is the significant one. Maps to
MaidrLayer.thresholdOptions.significanceDirection.
'above' suits the transformed axes these charts usually carry; a raw p
axis runs the other way and needs 'below', where a reading fixed to
'above' would select precisely the points that failed to reach
significance and announce them as the result.
The grammar's 'above' default is the grammar's to apply: pass your value
through or pass nothing.
OptionaleffectThe effect-size cutoff on the x axis, applied to its magnitude. Maps
to MaidrLayer.thresholdOptions.effect.
Meaningful on a volcano, whose x is an effect size. A Manhattan's x is a genomic position and its x-axis plot lines are chromosome dividers rather than cutoffs, so this is never inferred for one — declare it or leave it out.
TraceType.VOLCANO — the string 'volcano'.
OptionalmergeAbsorb following undeclared siblings of the same drawn kind, as ManhattanDeclaration.merge does.
Off by default, the other way round from a Manhattan: a volcano's sibling series are usually up-regulated, down-regulated and unchanged — three things a reader wants told apart, not one cloud.
Effect size against significance — the standard figure of a differential expression analysis.
The same chart as a ManhattanDeclaration, read the same way and accepting the same fields:
labelnames the gene the way it names the SNP, andsignificanceis the same cutoff on the same axis. What a volcano adds is the second cutoff — its x is an effect size rather than a position, so a point is a finding only when it clears both.