Skip to main content

SharedGCContentDisplay

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the gccontent plugin. View source.

Shared config for the two GC content displays: LinearGCContentDisplay (on a ReferenceSequenceTrack, deriving GC from the track's own sequence adapter) and LinearGCContentTrackDisplay (on a standalone GCContentTrack). Both register the same slots against different track types, so the slots live here once; a config always names one of the two concrete types.

Config slots

SharedGCContentDisplay is a shared base schema, not a type you name in a config. Set these slots on one of the configs under Extended by above, each of which lists them as inherited and shows the shape in its own example. 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
windowSize
number = 100		Number of bases per GC measurement window.
windowDelta
number = 100		Step between successive windows; smaller than windowSize means overlapping windows (a smoother signal).
gcMode
stringEnum (content, skew) = 'content'		content for GC percentage, skew for (G-C)/(G+C) strand skew.
summaryScoreMode
stringEnum (max, min, avg, whiskers) = 'avg'		GCContentAdapter never emits real per-bin min/max, so the inherited 'whiskers' default has no summary to draw — it just forces posColor-only rendering (buildSourceRenderData skips the bicolor pos/neg split for whiskers) and hides negative GC-skew as if it were positive
Inherited from LinearWiggleDisplay22 slots
defaultRendering
stringEnum (xyplot, density, line, linecenter, scatter) = 'xyplot'		Default rendering type: xyplot, density, line, linecenter, or scatter.
{
  "type": "LinearWiggleDisplay",
  "defaultRendering": "density"
}
height
number = 100		Default height of the track
useBicolor
boolean = true		When true (the default), positive scores use posColor and negative use negColor; when false, all bars use the single color slot. Setting color alone, with no posColor/negColor/useBicolor, turns this off for you.
color
color = '#0068d1'		Single fill CSS color for the wiggle bars; a wiggle colors per signal, not per feature, so jexl callbacks do not apply. Set alone it implies useBicolor false; alongside posColor/negColor it goes unused. Density rendering always draws from posColor.
scoreRules
frozen = []		Not in the shared wiggle fields: MultiLinearWiggleDisplay spreads those and stacks a plot box per row, so one rule list has no single axis to sit on there.
minimalTicks
boolean = false		Draw only the min/max Y-axis ticks
advanced
minScore
number = Number.MIN_VALUE		Fixed minimum score bound. The default (Number.MIN_VALUE) is a sentinel meaning "unset, use autoscale"
advanced
maxScore
number = Number.MAX_VALUE		Fixed maximum score bound. The default (Number.MAX_VALUE) is a sentinel meaning "unset, use autoscale"
advanced
scaleType
stringEnum (linear, log, symlog) = 'linear'		Scale type. "log" cannot represent 0 or negative scores and floors the domain above them; "symlog" is log-like away from zero and linear through it, so a track whose scores touch or cross 0 keeps them
autoscale
stringEnum (local, localsd, localpercentile) = 'localpercentile'		Autoscale type: "local" uses the min/max in the visible region, "localsd" uses mean ± numStdDev standard deviations, "localpercentile" uses the numQuantile-th percentile score as the max (robust to skewed/peaky data)
numStdDev
number = 3		Number of standard deviations to use for the localsd autoscale type
advanced
displayCrossHatches
boolean = false		Rule the score axis with horizontal cross hatches at the tick positions — the config form of the score menu's "Show cross hatches". Ignored by the density rendering types, which spend color rather than height on the score and so have no axis to rule
symlogConstant
number = 0		Width of symlog's linear region around zero. The default 0 means "derive from the domain" (a thousandth of its largest magnitude). Setting it to 1 makes symlog exactly log(x+1), which flattens anything living below 1 — set it near the smallest score you need to tell apart instead
advanced
posColor
color = '#0068d1'		Fill color for positive scores, used when useBicolor is true (the default)
negColor
color = '#e01e26'		Fill color for negative scores, used when useBicolor is true (the default)
bicolorPivot
number = 0		Pivot value for bicolor mode
advanced
numQuantile
number = 0.99		Percentile used to clip outliers for the localpercentile autoscale type (e.g. 0.99 clips the outermost 1% of each sign). Positive and negative extents are computed independently and anchored at 0, so a sparse minority tail (e.g. phyloP acceleration) stays visible; all-positive data pins the min at 0
advanced
scatterPointSize
maybeNumber = 2 promotable		Point height in px for scatterplot ("scatter"/"multiscatter") rendering. Unset (the default) follows the session-wide default for this display type, falling back to 2
advanced
lineWidth
maybeNumber = 1 promotable		Line thickness in px for line ("line"/"multiline") rendering. Unset (the default) follows the session-wide default for this display type, falling back to 1
advanced
maxGapMultiple
number = 0		Interpolated line ("linecenter"/"multilinecenter"/"multirowlinecenter") only: break the line where consecutive points sit further apart than this multiple of the track's own mean point spacing, instead of drawing one long chord across the hole. Scaled to the data rather than a fixed bp distance so it holds at every zoom. 0 disables breaking (the pre-existing behavior, one connected line throughout)
advanced
fetchSizeLimit
number = 1_000_000		maximum data to attempt to download for a given track, used if adapter doesn't specify one
advanced
forceLoad
boolean = false		Declarative equivalent of the "Force load" button on the "too much data" banner: when true the display always renders, however large the region or dense the features. Off by default (the gate guards against huge downloads). Set it on a view no one can interact with — an embedded / notebook view, or a screenshot — where the region is known and you want it drawn without a click.
advanced