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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.

The Hi-C display's encoding.color: a bin's observed contact count, or its observed/expected or observed/control ratio, through a linear, symlog or log scale.type onto a named scale.scheme.

  • observed: an unset scale.domainMax follows the loaded counts, saturating at their scale.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.
  • observed/expected: each count over the file's expected count at that distance, the view Juicebox calls O/E, which shows compartments and loops under the decay of contact with distance. It diverges around 1 from a quarter to fourfold, and where the file has no expected values at the binsize, the display paints the counts and the key says so.
  • observed/control: each count over the adapter's controlAdapter count for the same bins, both scaled to the two libraries' common depth and given a pseudocount of 1. A cell only one condition holds draws too, so lost and gained contacts both show; on the same ramp as observed/expected.

The slots are the shared color channel's, so jbrowse validate and "Edit plot..." judge them as they judge any other display's.

Example usage

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

Preset fields

A field named here paints through its own scale while scale.type is unset, and range and names index its levels in order while domain is unwritten.

FieldScaleLevelsNamesOther defaults
observedlinearscheme: juicebox; key "Contacts"
observed/expectedlogscheme: redblue; reverse: true; domainMin: 0.25; domainMax: 4; domainMid: 1; key "Observed/expected"
observed/controllogscheme: redblue; reverse: true; domainMin: 0.25; domainMax: 4; domainMid: 1; key "Observed/control"

Config slots

A setting written to it replaces it whole: a member left out returns to its default. 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 (observed, observed/expected, observed/control) = 'observed'		observed, each bin's contact count; observed/expected, that count over the file's expected count at its distance; or observed/control, that count over the control file's, both scaled to one library depth
scale
HicColorScale sub-schema		How a bin's value maps to a color, Vega-Lite's scale object.
scale.type
maybeStringEnum (linear, symlog, log)		linear; symlog, d3's log(1 + count), which the Log scale toggle writes: it lifts sparse long-range bins off the floor, so only 0 paints as the domain's bottom does; or log, log2 of the count from a pinned domainMin or else 1, every bin at or below which paints as the domain's bottom does. Juicebox paints that bottom transparent. Unset is the field's own, linear for observed
scale.scheme
maybeStringEnum (viridis, magma, inferno, cividis, juicebox, fall, reds, blues, redblue, purpleorange, redgreyblue, redyellowblue)		the named ramp the field runs across; unset is the field's own, juicebox for count, which fades from transparent to red
scale.reverse
maybeBoolean		Unset turns round viridis, magma, inferno and cividis, which run dark at their low end, since an unpainted bin is the page behind the matrix; the field's own scheme keeps the field's direction.
scale.domainMid
colorRampSlots.domainMid		The value the ramp's middle stop sits at, so a diverging scheme centres on it and equal distances from it take equal colors; unset, the stops spread evenly across the domain.
scale.domainMin
maybeNumber		the bottom of the scale; unset follows the loaded values, whose extent starts at 0 since no value is below it
scale.domainMax
maybeNumber		the top of the scale's domain; unset follows the loaded counts
scale.domainQuantile
number = 0.95		The value an unset domainMax follows: the loaded values' quantile, 0.95 so faint off-diagonal contacts read, or at 1 their maximum. The track menu's "Emphasize faint contacts" toggles it. Only the top clips, since the values' extent starts at 0, the way an axis that starts at 0 adds 0 to the shared quantile extent.
legend
HicColorLegend sub-schema		The key this channel draws: title replaces the heading naming the field and binsize, and "" draws none.
legend.title
maybeString		key title; unset keeps the display's own heading, "" draws none