trans_matrixplot: Trans matrix plot

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

Trans matrix plot

Description

This function plots a matrix of contacts data for the intersection of two regions. Using two regions on different chromosomes plots trans data.

Usage

trans_matrixplot(
  exp1,
  exp2 = NULL,
  chrom_up,
  start_up,
  end_up,
  chrom_down,
  start_down,
  end_down,
  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 subtracted from the exp1 data.
chrom_up, chrom_down	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_up, start_down	An integer with the start position of the regions of interest.
end_up, end_down	An integer with the end position of the regions of interest.
colour_lim	A numeric of length two giving the minimum and maximum values in contacts. 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.

Value

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

Resolution recommendation

A resolution in the ballpark of (end - start) / 500.

See Also

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

Examples

## Not run: 
trans_matrixplot(exp, 
                 chrom_up = "chr1:30,000,000-40,000,000",
                 chrom_down = "chr2:50,000,000-60,000,000")

## End(Not run)

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