borderplot-methods: Plots of Border Elements

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 positive and negative feature intensities.

Usage

borderplot(x, type = c("pos", "neg"), qualopt = "raw", transfo = log2, range = 0, names = "namepart", ylim = NULL, bmar = NULL, las = 2, ...)

Arguments

x	object of class QualTreeSet.
type	type of border elements to be used, one of “pos”, “neg”, or both.
qualopt	character string specifying whether to draw boxplots for “raw”, “adjusted”, or “normalized” border intensities.
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.
ylim	the y limits of the plot.
bmar	optional list for bottom margin and axis label magnification cex.axis.
las	the style of axis labels.
...	optional arguments to be passed to borderplot.

Details

Creates a boxplot of the positive and negative feature intensities for an object of class QualTreeSet.

For names=NULL full tree names will be displayed while for names="namepart" tree names will be displayed without name extension. If names is a vector of tree 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 b and axis label magnification cex.axis will be adjusted depending on the number of label characters and the number of samples.

Author(s)

Christian Stratowa

See Also

plotBorder, coiplot

Examples

## Not run: 
 ## border intensities, created by e.g. rmaPLM()
 getTreeNames(rootFile(rlm.all), treetype="brd")
 borderplot(rlm.all)
 borderplot(rlm.all, type="pos")
 borderplot(rlm.all, type="neg")

## End(Not run)

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