rangeCoveragePlot {BindingSiteFinder}R Documentation

Plot crosslink events coverage over range

Description

A diagnostic plot function that allows to check the coverage of crosslink events over different merged regions. The coverage is shown as mean over all replicates and conditions, with a standard deviation corridor.

Usage

rangeCoveragePlot(object, width, name = "Coverage Plot", ...)

Arguments

object

a BSFDataSet, or a list of BSFDataSet

width

a numeric value that defines the plotting ranges

name

plot title

...

further arguments passed to ggplot

Details

If object is a single BSFDataObject a single coverage plot will be drawn, whereas if it is a list of BSFDataObjects, then faceting is used to make a plot for each list element.

Value

a plot of type ggplot2 displaying the crosslink coverage over the ranges of the given BSFDataSet

See Also

BSFDataSet

Examples

# load data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))

# plotting a single object
bds <- makeBindingSites(object = bds, bsSize = 9, minWidth = 2,
minCrosslinks = 2, minClSites = 1)
rangeCoveragePlot(bds, width = 20)

# plotting multiple objects
bds1 <- makeBindingSites(object = bds, bsSize = 3, minWidth = 2,
minCrosslinks = 2, minClSites = 1, sub.chr = "chr22")
bds2 <- makeBindingSites(object = bds, bsSize = 9, minWidth = 2,
minCrosslinks = 2, minClSites = 1, sub.chr = "chr22")
l = list(`1. bsSize = 3` = bds1, `2. bsSize = 9` = bds2)
rangeCoveragePlot(l, width = 20)


[Package BindingSiteFinder version 1.0.0 Index]