TEQC (version 3.12.0)

coverage.plot: Coverage versus base position plot

Description

Line plot of per-base coverages along a genomic region. Position of target regions can be shown.

Usage

coverage.plot(coverageAll, targets, chr, Start, End, Offset = 0, add = FALSE, col.line = 1, col.target = "orange", col.offset = "yellow", xlab, ylab, ylim, ...)

Arguments

coverageAll

RleList containing Rle vectors of per-base coverages for each chromosome, i.e. coverageAll output from coverage.target

targets

optional; RangedData table containing positions of target regions, i.e. output from get.targets; if missing no genomic regions are highlighted

chr

on which chromosome the region to plot is located (string, e.g. "chr1")

Start

genomic position where to start the plot

End

genomic position where to end the plot

Offset

integer; highlight Offset bases on both sides of each targeted region; defaults to 0

add

if TRUE, the coverage line of a new sample is added to an already existing plot

col.line

color of the coverage line

col.target

color of the bar indicating target regions

col.offset

color for highlighting Offset on the sides of target regions

xlab, ylab

x- and y-axis labels

ylim

y-axis coordinate ranges

...

further graphical parameters, passed to plot

Value

When positions of target regions are provided, a bar on the bottom indicates their location such that coverage can be related to the captured targets.

Details

If coverage of a new sample is added to an existing plot with add = TRUE, parameters chr, Start, End still have to be specified and should be the same as in the previous call in order to make sense. Parameters targets and Offset can but do not have to be given again. They can also differ from the previous ones, if for the additional sample a different target was captured.

See Also

coverage.target, make.wigfiles, covered.k, coverage.hist, coverage.uniformity, coverage.targetlength.plot

Examples

## get reads and targets
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
targets <- get.targets(targetsfile, skip=0)

## calculate per-base coverages
Coverage <- coverage.target(reads, targets, perBase=TRUE)

## coverage plot
coverage.plot(Coverage$coverageAll, targets, Offset=100, chr="chr1", Start=11157524, End=11158764)