Skip to main content

HicData

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

What a Hi-C display's fetch reads of the file: resolution steps the binsize from the one the zoom picks, and normalization is the matrix normalization asked for.

Example usage

One binsize finer than the zoom picks, with vanilla coverage:

{
  "type": "LinearHicDisplay",
  "data": { "resolution": 1, "normalization": "VC" }
}

Config slots

A setting written to it names members one by one: a member left out stays as it is, and null resets one. 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
resolution
number = 0		binsizes finer than the zoom picks: 1 one finer, -1 one coarser, 0 follows the zoom
normalization
string = 'KR'		preferred matrix normalization (KR, SCALE, VC, VC_SQRT, NONE); a scheme the file lacks falls back to one it has