xps (version 1.32.0)

borderplot-methods: Plots of Border Elements

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.

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)