plotSegment {nullranges}R Documentation

Plot genome segmentation

Description

Plot genome segmentation

Usage

plotSegment(
  seg,
  exclude = NULL,
  type = c("ranges", "barplot", "boxplot"),
  region = NULL
)

Arguments

seg

the segmentation GRanges returned by segmentDensity function

exclude

GRanges of excluded region

type

the type of plot returned. Choices are segmentation plot included ranges information, barplot showing segmentation states' distribution across chromosome, or a box plot indicating average density within each states. Default is all plots are displayed. The y axis "density" represent square root of overlap counts within segment length. If a user defined segmentation GRanges is given, the y axis is default to be 1 for all states in segmentation plot.

region

GRanges of stricted region that want to be plotted.

Value

A ggplot set by type argument

Examples


example("segmentDensity")
plotSegment(seg, exclude, type = "ranges")
plotSegment(seg, exclude, type = "barplot")
plotSegment(seg, exclude, type = "boxplot")
[Package nullranges version 1.0.1 Index]