plot.SpliceExprSet: plot a SpliceExprSet

In splicegear: splicegear

Description

Plot a object of class SpliceExprSet

Usage

## S3 method for class 'SpliceExprSet'
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

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.

Value

function used for its side-effect(s).

Author(s)

laurent

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)

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