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HicColor

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the hic plugin. View source.

Example usage

{
  type: 'LinearHicDisplay',
  color: { scale: 'log', scheme: 'viridis', domainMax: 500 },
}

The Hi-C display's color: a bin's contact count through a linear or log scale onto a named scheme. An unset domainMax follows the loaded counts, saturating at their domainQuantile, the 95th percentile by default, or at their maximum at a quantile of 1; setting it gives every zoom, and every track that sets the same number, one scale. The slots are the shared color object's, so jbrowse validate and "Edit plot..." judge them as they judge any other display's.

Config slots

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
field
stringEnum = 'count'		count, each bin's contact count
scheme
stringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue, blueyellowred) = 'juicebox'		the named ramp counts run across; juicebox fades from transparent to red
reverse
maybeBoolean		Unset turns round a scheme dark at its low end, since an unpainted bin is the page behind the matrix.
domainMin
maybeNumber		the bottom of the scale; unset is 0
domainQuantile
number = 0.95		The value an unset domainMax follows: the loaded counts' quantile, 0.95 so faint off-diagonal contacts read, or at 1 their maximum. The track menu's "Emphasize faint contacts" toggles it. The same word every color ramp and scales.y take.
scale
maybeStringEnum (linear, log)		linear, or log2 of the count, which lifts sparse long-range bins off the floor; unset is linear
domainMax
maybeNumber		the top of a linear or log scale's domain; unset follows the loaded values