insulation_matrixplot: Insulation matrix plot.

In robinweide/GENOVA: GENOVA: expore the Hi-C

Insulation matrix plot.

Description

Display a Hi-C matrix with insulation scores annotated in the margins.

Usage

insulation_matrixplot(
  exp1,
  exp2 = NULL,
  IS_discovery = NULL,
  chrom,
  start,
  end,
  colour_lim = NULL,
  rasterise = FALSE,
  colour_bar = FALSE
)

Arguments

exp1	A GENOVA contacts object.
exp2	A GENOVA contacts object compatible with exp1 (optional) or NULL. If not NULL, the exp2 argument will be displayed alongside the exp1 data.
IS_discovery	A IS_discovery object, as created by the insulation_score function. When NULL, the insulation score will be calculated on the fly for this region only.
chrom	One of the following: A character of length 1 giving the chromosome name of the region of interest. A 3-column, 1-row data.frame in BED-format. A single character describing a locus in UCSC notation, e.g. "chr1:30,000,000-40,000,000". The latter two options automatically provide the start and end arguments too.
start, end	An integer with the start- and end-positions of the region of interest in basepairs.
colour_lim	A numeric of length two giving the minimum and maximum values in contact values. Out of bounds values will be set to the nearest limits.
rasterise	Set to TRUE to use a bitmap raster instead of polygons.
colour_bar	A logical of length 1, indicating whether a colour-bar legend should be drawn at the right.

Details

The 'on-the-fly' calculation of the insulation score uses the default settings. Therefore, if for example the window size is to be changed, please use the insulation_score() function and provide the result as the IS_discovery argument in this function.

Because the 'on-the-fly' calculation of the insulation score only computes the insulation score for this locus, there might a small offset to the scores due to the limited scope for normalisation.

Value

No values are returned but a plot is outputted on the graphics device.

Recommended resolution

10kb-40kb

See Also

The insulation_score function for computation of insulation scores.

Other matrix plots: compartment_matrixplot(), hic_matrixplot(), pyramid(), trans_matrixplot()

Examples

## Not run: 
insulation_matrixplot(
  WT_20kb, KO_20kb,
  chrom ="chr1:40,000,000-60,000,000"
)

## End(Not run)

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.