splicegear (version 1.44.0)

grid.plot.Probes: 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(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.

probes.opt

options to plot the probes

fig.xratio

ratio for the left and right parts of the plot

fig.yratio

ratio for the upper and lower parts of the plot

vp

a viewport (grid package stuff)

xlim

range for the x-axis (see plot).

ylim

range for the y-axis

...

optional parameters

Value

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

Details

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

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)