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

In LTLA/fugi: Further Utilities for Genomic Interactions

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 GenomicInteractions object generated by viewPoint.
left_dist	Integer scalar specifying the distance to the left of each bait to consider, in bp.
right_dist	Integer scalar specifying the distance to the right of each bait to consider, in bp.
ylab	String containing the Y axis label.
xlab	String containing the X axis label.
fix	One of "center", "start", "end", to be passed to resize. Interaction distances are calculated relative to this part of the bait.
...	Additional arguments to plot.

Value

A coverage track is plotted on the current graphics device. A RleList object containing the aggregated coverage is invisibly returned.

Examples

data(hic_example_data)
hic_example_data <- updateObject(hic_example_data)

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)

LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.