plot.SpliceSites: plot a SpliceSites object
In splicegear: splicegear

Description Usage Arguments Details Value Author(s) References See Also Examples

plot objects.

## S3 method for class 'Probes'
plot(x, col="black",
            xlab = "sequence", ylab = "probes",   
            add=FALSE, probepos.yscale=NULL, xlim=NULL,
            ...)
## S3 method for class 'SpliceSites'
plot(x, col.typeI = "orange",
            col.typeI.window = "yellow",
            col.typeII = "red",
            add=FALSE, ylim=NULL, ...)

`x`	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`.

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.

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

Laurent

"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.

SpliceSites-class

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))