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LinearHicDisplay

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

Draws a HicTrack's contact matrix as a triangular heatmap in the linear genome view, at a bin size that follows the zoom.

Example usage

A log color scale, one binsize coarser than the zoom picks, through the displayDefaults shorthand. See the Hi-C track guide for the rest:

{
  type: 'HicTrack',
  trackId: 'hic',
  name: 'Hi-C',
  assemblyNames: ['hg38'],
  adapter: { type: 'HicAdapter', uri: 'https://example.com/contacts.hic' },
  displayDefaults: {
    encoding: { color: { scale: { type: 'symlog' } } },
    data: { resolution: -1 },
  },
}

Overview

LinearHicDisplay - Identifier

Every LinearHicDisplay has a unique displayId, a required top-level field that identifies it (not one of the config slots below).

Color channels

Setting Page scale.type Preset fields
encoding.color HicColor linear, symlog, log observed, observed/expected, observed/control

Config slots

Display slots go on a display entry: "displays": [{ "type": "LinearHicDisplay", ... }], 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.

Slot Description
encoding
HicEncoding		 The channels the bins paint through: encoding.color, the scale from count to color.
legend
HiddenLegend		 The color ramp's key, off until asked for.
data
HicData		 What the fetch reads, a HicData object: resolution steps the binsize from the zoom's pick, normalization names the matrix normalization.
filter
list of FieldPredicate entries		 Floors, written gte or gt, on the counts a cell is built from: observed, the map's count, and under observed/control control, the control's, both before the depth scaling. A cell below a floor is left out before its ratio, so a ratio of two near-empty bins does not speckle the triangle. A floor on observed alone drops the contacts a condition lost; floor control, or both, to keep them.
height
number = 300		 default height for the Hi-C track
heightMode
stringEnum (fixed, fit) = 'fixed'		 fixed draws square cells at the triangle's natural half-width height; fit squashes it to fill the display height

Retired keys

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.

Key On load
maxFeatureScreenDensity ignored
maxDisplayedBpPerPx ignored
fetchSizeLimit ignored
mouseover ignored
jexlFilters moved into a current slot
renderer ignored