grid.plot.Probes {splicegear}R Documentation

Plot splicegear objects

Description

Plot objects defined in the package splicegear

Usage

grid.plot.Probes(x, col = "black", add = FALSE, probepos.yscale = NULL,
              xlim = NULL, vp = NULL, ...)

grid.plot.SpliceSites(x, col.typeI = "orange", col.typeI.window = "yellow", 
    col.typeII = "red", add = FALSE, ylim = NULL, vp = NULL, 
    ...)

grid.plot.SpliceExprSet(function (x, probes.opt = list(), expr.opt = list(col = NA, lty = 1:6),
    fig.xratio = c(2, 1), fig.yratio = c(2, 1), probepos.yscale = NULL,
    ylim = NULL, ...)

Arguments

x object of Probes-class, SpliceSites-class or SpliceExprSet-class
add add to an existing plot
col color(s) for the probes (recycled if necessary).
col.typeI color(s) for the type I spliced out exons
col.typeI.window background color for the type I spliced out `windows'
col.typeII color for the type II splicing events
expr.opt list of options to plot expression values
probepos.yscale specify coordinates on the y-axis for the probes.
vp a viewport (grid package stuff)
xlim range for the x-axis (see plot).
ylim range for the y-axis
... optional parameters

Details

The `type I'/'type II' thing is described in the references found in the help files for plot.SpliceSites.

Value

These functions are mainly used for their side effects. grid.plot.SpliceSites returns the range for the y-axis when needed.

See Also

plot.SpliceSites, plot.Probes

Examples

## plot splice sites
data(spsites)
grid.plot(spsites)

## plot probes
data(probes)
grid.plot(probes)

## combined plot
grid.plot(probes, spsites)


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