R: plot a SpliceSites object

plot.SpliceSites {splicegear}

R Documentation

plot a SpliceSites object

Description

plot objects.

Usage

## 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, ...)

Arguments

`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`.

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.

Value

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

Author(s)

Laurent

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

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))

[Package splicegear version 1.54.0 Index]