Skip to main content

HicColor

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

Example usage

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

See the Config slots section below for all available configuration fields.

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.

Config slots

These slots go on a display entry: "displays": [{ "type": "HicColor", ... }], or in the track's displayDefaults when this is its default display. 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
scale
stringEnum (linear, log) = 'linear'		linear, or log2 of the count, which lifts sparse long-range bins off the floor
scheme
stringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange) = '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.
domainQuantile
number = 0.95		What 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 colour ramp and scales.y take.
domainMin
maybeNumber		the bottom of a linear or log scale's domain; unset follows the loaded values
domainMax
maybeNumber		the top of a linear or log scale's domain; unset follows the loaded values