GenomicInteractions (version 1.6.2)

plotAvgViewpoint: 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

Run this code
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)

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