rangeCoveragePlot: Plot crosslink event coverage over binding site range

In ZarnackGroup/BindingSiteFinder: Binding site defintion based on iCLIP data

Plot crosslink event coverage over binding site 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 = 20,
  show.samples = FALSE,
  subset.chromosome = "chr1",
  quiet = TRUE
)

Arguments

object	a BSFDataSet, or a list of BSFDataSet
width	numeric; set the plotting range to show (in nt)
show.samples	logical; to show individual samples as lines
subset.chromosome	character; subset by a all ranges on the indicated chromosome. Can also be a vector with multiple chromosomes. If NULL then all ranges are being used.
quiet	logical; whether to print messages

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, makeBindingSites

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, subset.chromosome = "chr22")

# 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, subset.chromosome = "chr22")

ZarnackGroup/BindingSiteFinder documentation built on Nov. 24, 2024, 10:41 a.m.