plot.SpliceExprSet: plot a SpliceExprSet

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/plot.SpliceExprSet.R

Description

Plot a object of class SpliceExprSet

Usage

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## 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

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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.