xps (version 1.32.0)

boxplot-methods: Box Plots

Description

Produce box-and-whisker plot(s) of the samples.

Usage

boxplot(x, which = "", size = 0, transfo = log2, range = 0, names = "namepart", bmar = NULL, ...)

Arguments

x

object of class DataTreeSet, ExprTreeSet or QualTreeSet.

which

type of probes to be used, for details see validData.

size

length of sequence to be generated as subset.

transfo

a valid function to transform the data, usually “log2”, or “0”.

range

determines how far the plot whiskers extend out from the box.

names

optional vector of sample names.

bmar

optional list for bottom margin and axis label magnification cex.axis.

...

optional arguments to be passed to boxplot.

Details

Creates a boxplot for slot data for an object of class DataTreeSet, ExprTreeSet or QualTreeSet.

For names=NULL full column names of slot data will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of column names, only these columns will displayed as boxplot.

For bmar=NULL the default list bmar = list(b=6, cex.axis=1.0) will be used initially. However, both bottom margin and axis label magnification will be adjusted depending on the number of label characters and the number of smaples.

See Also

plotBoxplot, boxplot

Examples

## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

## need to attach scheme mask and probe intensities only if "userinfo" is not used
data.test3 <- attachMask(data.test3)
data.test3 <- attachInten(data.test3)

if (interactive()) {
boxplot(data.test3)
}

## optionally remove mask and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeMask(data.test3)

## alternatively use the quantiles stored in userinfo of trees
if (interactive()) {
boxplot(data.test3, which="userinfo:fIntenQuant")
}

rm(scheme.test3, data.test3)
gc()