plot.SpliceSites {splicegear}R Documentation

plot a SpliceSites object

Description

plot objects.

Usage

plot.Probes(x, col="black",
            xlab = "sequence", ylab = "probes",   
            add=FALSE, probepos.yscale=NULL, xlim=NULL,
            ...)
plot.SpliceSites(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.

See Also

SpliceSites-class

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 1.4.0 Index]