plot.SpliceSites: plot a SpliceSites object

Description

plot objects.

Usage

"plot"(x, col="black", xlab = "sequence", ylab = "probes",    add=FALSE, probepos.yscale=NULL, xlim=NULL, ...)
"plot"(x, col.typeI = "orange", col.typeI.window = "yellow", col.typeII = "red", add=FALSE, ylim=NULL, ...)

Arguments

object of class Probes or SpliceSites.

col

color argument for the probes.

col.typeI

color argument for the type I splice sites

col.typeI.window

color argument for the type I `window'

col.typeII

color argument for the type II splice sites

add

add the plot to an existing plot. Make a new plot if `FALSE'

probepos.yscale

scaling argument

xlim, ylim

range of plotting window

xlab, ylab

labels for the axis

...

optional parameters to be passed to the function plot.

Value

The range for the y-axis is returned whenever needed (see invisible).

Details

If the parameter main is not specified, the function tries to extract the attribute `name' from x. The two functions can be combined to display both objects on the same plot.

References

"Standardized output for putative alternative splicing; a R package as an application to combine them with microarray data", Gautier L. Dao C. and Yang U.C., 2003, submitted.

Examples

Run this code

data(spsites)

plot(spsites, main=attr(spsites, "name"))

sp.pData <- spsites@spsiteIpos.pData

##col <- as.integer(factor(sp.pData$tissue))

##plot(spsites, col.typeI=col, main=attr("name", spsites))

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