plotDistributions {arrayMagic}R Documentation

Visualise Distributions

Description

Boxplot like visualisation of distributions, only the boxes, i.e. the median and roughly the second and third quartile are plotted (cf. boxplot.stats). The plots may help to identify shortcomings of the raw data or normalised data. The argument quantiles can be used to visualize two or three arbitrary quantiles with boxes.

Arguments

dataMatrix data matrix, where columns represent distributions, e.g. raw array data, log(raw array data) or normalised data
transFunc data transformation function, e.g. log
quantiles missing by default; a vector of two or three increasing quantiles used to determine the boxes to be drawn
title plot title, type character string
labels vector of names, may substitute column names of dataMatrix
xAxisLabel label for x axis
yAxisLabel label for y axis
colourVector vector of colours
width graphics window width
height graphics window height
plotOutput character string specifying either "screen" or "pdf"; default: "screen"

Details

Default of transFunc is no transformation, i.e. identity. If labels are supplied at first the column names or secondly a numbering are used instead.By default the colourVector is defined as alternating darkred and darkgreen.

Value

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

boxplot.stats

Examples

plotDistributions(cbind(rnorm(100),rnorm(100)), title="Random Gaussians", labels = c("N1","N2"), yAxisLabel="scale")
          plotDistributions(as.matrix(1:100), quantiles=c(0.25,0.85),title = "Random Gaussians", labels = c("N1"), yAxisLabel = "scale")

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