splicegear (version 1.44.0)

plot.SpliceExprSet: plot a SpliceExprSet

Description

Plot a object of class SpliceExprSet

Usage

"plot"(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, ...)

Arguments

x

a SpliceExprSet-class

probes.opt

optional parameters to be passed for the plotting of the Probes-class

expr.opt

optional parameters to be passed for the plotting of the ExpressionSet-class

fig.xratio

ratio between the left and right parts of the plot

fig.yratio

ratio between the upper and lower parts of the plot

probepos.yscale

enforce `y' positions for the probes.

ylim

range for the y-axis

...

optional parameters to be passed to the function plot

Value

function used for its side-effect(s).

Details

The argument probepos.yscale can be used to scale probes according to their position on the reference sequence, as shown in the last example below.

See Also

SpliceExprSet-class

Examples

data(spliceset)


levels(pData(spliceset@eset)$Material)
## Liver, Mix and SNB19
cl.mat <- c("red", "yellow","blue")[as.integer(pData(spliceset@eset)$Material)]
## colored in red, yellow and blue respectively
plot(spliceset, expr.opt = list(col = cl.mat, log = "x"))

## sort
spliceset <- sort.SpliceExprSet(spliceset)
begin.pos <- spliceset@probes@pos[, 1]
plot(spliceset, expr.opt = list(col=cl.mat), probepos.yscale = begin.pos)