plotAvgViewpoint: Plot coverage around a set of virtual 4C viewpoints

In ComputationalRegulatoryGenomicsICL/GenomicInteractions: Utilities for handling genomic interaction data

Plot coverage around a set of virtual 4C viewpoints

Description

Plots summarised coverage of interactions around a set of viewpoints, e.g. promoters. This function requires the output of 'viewPoint()' as input.

Usage

plotAvgViewpoint(
  x,
  left_dist = 1e+05,
  right_dist = 1e+05,
  ylab = "Average signal",
  xlab = "Relative position",
  fix = "center",
  ...
)

Arguments

x	A GInteractions object which is output from viewPoint
left_dist	Distance 'left' of interactions to consider, in bp.
right_dist	Distance 'right' of interactions to consider, in bp.
ylab	Y axis label.
xlab	X axis label.
fix	One of 'center', 'start', 'end'. Passed to 'resize'. Interaction distances are calculated relative to this part of the bait.
...	additional arguments to plot

Value

Coverage that is plotted (invisibly)

Examples

data(hic_example_data)
library(GenomicRanges)
pos <- GRanges(seqnames='chr15', ranges=IRanges(start=59477709, end=59482708))
region <- GRanges(seqnames='chr15', ranges=IRanges(start=58980209, end=59980208))
vp <- viewPoint(hic_example_data, pos, region)
plotAvgViewpoint(vp, left_dist = 1000000, right_dist = 100000)

ComputationalRegulatoryGenomicsICL/GenomicInteractions documentation built on April 16, 2022, 4:09 a.m.