plotSegment: Plot genome segmentation

In nullranges/nullranges: Generation of null ranges via bootstrapping or covariate matching

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")

nullranges/nullranges documentation built on Aug. 29, 2023, 12:13 a.m.