plot.SpliceSites: plot a SpliceSites object

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

View source: R/plot.SpliceSites.R

Description

plot objects.

Usage

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## 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.

See Also

SpliceSites-class

Examples

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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))

splicegear documentation built on Oct. 31, 2019, 7:40 a.m.