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LinearHicDisplay

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

Example usage

A log colour scale, one step 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: { color: { scale: 'log' }, resolutionBias: 1 },
}

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

Overview

LinearHicDisplay - Identifier

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

Config slots

These 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.

SlotDescription
color
HicColor		How a count becomes a colour: a linear or log scale onto a named scheme, over a domain whose unset ends follow the loaded counts.
resolutionBias
number = 0		steps from the zoom-picked binsize: -1 one finer, +1 one coarser, 0 follows the zoom
showResolutionControls
boolean = false		show the on-figure resolution dropdown in the overlay
selectedNormalization
string = 'KR'		preferred matrix normalization (KR, SCALE, VC, VC_SQRT, NONE); a scheme the file lacks falls back to one it has
height
number = 300		default height for the Hi-C track
showLegend
boolean = false		show the color scale legend
squashToHeight
boolean = false		squash the triangle vertically to fill the display height instead of drawing square cells