grid.plot.SpliceSites: Plot splicegear objects

In splicegear: splicegear

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

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)

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