TEQC (version 3.12.0)

coverage.targetlength.plot: Number of reads or average coverage versus target length scatter plot

Description

Plots either numbers of on-target reads or average per-target coverage (or potentially other per-target values) against respective target lengths. A smoothing spline is added to the scatter plot.

Usage

coverage.targetlength.plot(targets, plotcolumn, linecol = 2, xlab, ylab, lwd, pch, cex, ...)

Arguments

targets

RangedData table containing positions of target regions and further 'values' columns that should be plotted, i.e. output from coverage.target or readsPerTarget

plotcolumn

name or index of column to plot (of the 'values' DataFrame within targets)

linecol

color of spline curve

xlab, ylab

x- and y-axis labels

lwd

line width of spline curve

pch

plotting character

cex

size of plotting character

...

further graphical parameters, passed to plot

Value

A smoothing spline is added to the plot.

Details

coverage.target and readsPerTarget can be used to calculate average per-target coverages and numbers of reads overlapping each target. The values are added to the RangedData table containing the target positions. Such RangedData table can then be used for plotting the calculated values against the respecitve target lengths.

See Also

coverage.target, readsPerTarget, covered.k, coverage.hist, coverage.uniformity, coverage.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)

## get average per-target coverage
Coverage <- coverage.target(reads, targets, perTarget=TRUE)
targets2 <- Coverage$targetCoverages

## get numbers of reads per target
targets2 <- readsPerTarget(reads, targets2)

## coverage vs target length
coverage.targetlength.plot(targets2, plotcolumn="avgCoverage", pch="o")

## coverage vs number of reads per target
coverage.targetlength.plot(targets2, plotcolumn="nReads", pch="o")