Plot genome segmentation

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")
#> 
#> sgmntD> n <- 10000
#> 
#> sgmntD> library(GenomicRanges)
#> 
#> sgmntD> gr <- GRanges("chr1", IRanges(round(
#> sgmntD+   c(runif(n/4,1,991), runif(n/4,1001,3991),
#> sgmntD+     runif(n/4,4001,4991), runif(n/4,7001,9991))),
#> sgmntD+   width=10), seqlengths=c(chr1=10000))
#> 
#> sgmntD> gr <- sort(gr)
#> 
#> sgmntD> exclude <- GRanges("chr1", IRanges(5001,6000), seqlengths=c(chr1=10000))
#> 
#> sgmntD> seg <- segmentDensity(gr, n=3, L_s=100, exclude=exclude, type="cbs")
#> Analyzing: Sample.1 
plotSegment(seg, exclude, type = "ranges")

plotSegment(seg, exclude, type = "barplot")

plotSegment(seg, exclude, type = "boxplot")