boxplot-methods: Box Plots

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

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.

Note

For a DataTreeSet object, data must first be attached using method attachInten.

Alternatively it is possible to use the pre-calculated quantiles stored in the userinfo of the data trees by calling which="userinfo:varlist", where the varlist to call is described in method treeInfo.

Author(s)

Christian Stratowa

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()

xps documentation built on Nov. 8, 2020, 6 p.m.