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.
Related links
- Extended by: LinearGCContentDisplay
- Extended by: LinearGCContentTrackDisplay
- Base config: LinearWiggleDisplay
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.
| Slot | Description |
|---|---|
windowSizenumber = 100 | Number of bases per GC measurement window. |
windowDeltanumber = 100 | Step between successive windows; smaller than windowSize means overlapping windows (a smoother signal). |
gcModestringEnum (content, skew) = 'content' | content for GC percentage, skew for (G-C)/(G+C) strand skew. |
summaryScoreModestringEnum (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 the above-origin colour on every bin (buildSourceRenderData skips the two-sided split for whiskers) and hides negative GC-skew as if it were positive |
| Inherited from LinearWiggleDisplay | 19 slots |
defaultRenderingstringEnum (xyplot, density, line, linecenter, scatter) = 'xyplot' | Default rendering type: xyplot, density, line, linecenter, or scatter. |
| facet Facet | One row per value of a field, stacked down the track with a label, a separator and the clustering sidebar. source — one row per subtrack — is the only field this display reads; leave it unset and every source is drawn in one shared plot. domain is the row order: the subtracks it names lead, the rest keep the adapter's order, and a clustering run rotates its dendrogram towards it rather than discarding it. |
| color WiggleColor | One CSS colour, or a field through a scale — score through threshold for the bicolor plot, through linear or log for the density ramp, source through categorical for a palette entry per subtrack. Unset, the layout decides: several sources in one plot box take a palette entry each, and anything else is the pos/neg pair about the origin. |
| scales ValueScale | The y scale the plot is drawn through: type, domainMin, domainMax, autoscale, numStdDev, numQuantile, symlogConstant and rules, the reference lines drawn across it. The density rendering draws no rule and does not widen to one: it spends colour on the score and has no axis to rule. |
showLegendboolean = true | Draw the key: density's score color ramp, or the source colors where several share one plot. Defaults to on |
minimalTicksboolean = false | Draw only the min/max Y-axis ticks advanced |
heightnumber = 100 | default height for the track |
scoreFieldstring = 'score' | Feature field plotted on the score axis, read natively off each feature. The default score is the field every adapter serves — including the value a BED adapter's scoreColumn rewrote it to — so an explicit name here reaches a raw column the adapter left alone (a BED extra column, a GFF attribute) and takes precedence over that adapter-tier rewrite. The Manhattan plot skips a feature with no finite value in the field; the wiggle renderings plot it at 0 |
displayCrossHatchesboolean = 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 |
resolutionnumber = 1 | how many points per pixel the fetch asks a tiered file for: 1 is one per pixel, larger is finer and smaller is coarser. Clamped to the range the Resolution menu offers, so a value outside it reads as the nearest end |
originnumber = 0 | The value bars grow from, and what a color scale reads where its own domain or domainMid is empty. The same slot, with the same meaning, as the mark display's origin |
scatterPointSizenumber = 2 | Point height in px for scatterplot rendering. Defaults to 2 advanced |
lineWidthnumber = 1 | Line thickness in px for line rendering. Defaults to 1 advanced |
maxGapMultiplenumber = 0 | Interpolated line 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 |
showTreeboolean = true | Show the subtrack clustering tree in the sidebar |
showBranchLengthboolean = true | position tree nodes by branch length (dendrogram) rather than evenly by topology (cladogram) |
showRowLabelsboolean = true | Name each subtrack row down the left edge |
treeAreaWidthnumber = 80 | width in px of the tree sidebar, which a drag on its edge also writes |
showRowSeparatorsboolean = false | draw a hairline between adjacent rows; off by default, because a painting whose neighbouring rows differ in color already separates itself and the line only earns its pixel where they do not — a run of same-colored rows reads as one block without it, with no way to recover the row count by eye. Drawn only once rows are at least 4px tall: below that the line is as thick as the row it borders, turning a dense painting into a grid of hairlines with a little color between them |