les (version 1.22.0)

plot,Les-method: plot method for class Les

Description

The 'plot' method plots the estimates of the 'les' package along the genome. This includeds $Lambda$ with confidence intervals and estimated regions.

Usage

plot(x, y, ...)
"plot"(x, y, chr, error="none", region=FALSE, limit=TRUE,
rug=FALSE, xlim, ylim=c(0, 1),  ...)

Arguments

x

Object of class 'Les', as returned by 'estimate', 'threshold' or 'ci'.

y

Annotation object, currently not used.

chr

Character or numeric specifying which chromosome to plot. Must have a match in 'chr' passed to 'Les'. A value is required if the probes are located on more than one chromosome.

error

Character string specifying if error estimates for $Lambda$ should be plotted (default: "none"). Valid values are "none" for no error estimates and "ci" for confidence intervals computed by the 'ci' method.

region

Logical indicating whether the estimated regions should be included in the plot. The 'regions' method must have been called beforehand.

limit

Logical specifying whether the estimated threshold $Theta$ should be indicated on the y-axis if estimated (default: TRUE).

rug

Logical whether the positions of the probes should be indicated along the x-axis (default: FALSE). For details see 'rug'.

xlim

Numeric vector with two elements specifying the range on the x-axis.

ylim

Numeric vector with two elements specifying the range on the y-axis.

...

Optional arguments used in order to customize the plot. See the ‘details’ section.

Details

This method provides high-level plotting for the 'Les' class.

The plot method uses a special system in order to customize the graphical elements of the figure. It allows to refer to the different components with the name of the additional input argument; its value is a list containing named graphical parameters for the underlying plot function. The following list describes the possible names and their contribution.

plotArgs

Arguments for the axis and the labeling, passed to the plot function.

borderArgs

Arguments for the border lines at $Lambda$ equal to 0 and 1, passed to the abline function.

errorArgs

Arguments for the confidence interval of $Lambda$, passed to the plotCI function of the gplots package.

probeArgs

Arguments for the representation of probes, passed to the points function.

limitArgs

Arguments for the horizontal line representing the threshold $Theta$, passed to the abline function.

sigArgs

Arguments for the representation of significant probes with $Lambda equal or greater Theta$, passed to the points function.

rugArgs

Arguments for the representation of the probe coverage along the genome, passed to the rug function.

regionArgs

Arguments for the representation of estimated LES, passed to the rect function. If 'col' is specified as a function it determines the color of each region depending on its input $Lambda$ (default: gray()). If 'col' is a vector its elements are used to color the regions with recycling.

See Also

Package: les-package

Class: Les Methods and functions: Les estimate threshold regions ci chi2 export plot

Examples

data(spikeInStat)

x <- Les(pos, pval)
x <- estimate(x, 200)
x <- threshold(x)
x <- regions(x)

plot(x, region=TRUE)