plotDistributions {arrayMagic}R Documentation

Visualisation of distributions

Description

Boxplot like visualisation of distributions, only the boxes, i.e. the median and the second and third quartile are plotted (cf. boxplot.stats for the details on the calculation). 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.

Usage

plotDistributions(dataMatrix, transFunc, quantiles, main, labels, xlab, ylab, colourVector, width=8, height=6, fileName="plotDistributionsOutput", savePath, plotOutput="standard", automaticSubtitle=TRUE)

Arguments

dataMatrix numeric data matrix, where columns represent distributions, e.g. raw array data or normalised data; required; default missing.
transFunc unary function; optional; default missing. 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
main plot title; type character string; optional; default missing
labels vector of names, may substitute column names of dataMatrix; optional; default missing
xlab label for x axis; type character string; optional; default missing
ylab label for y axis; type character string; optional; default missing
colourVector vector of colours; optional; default missing
width graphics window width; required; default: 8
height graphics window height; required; default: 6
fileName optional; default: "plotDistributionsOutput"
savePath optional; default: missing
plotOutput character string specifying either "standard", "screen", "pdf", "win.metafile"; default: "standard"
automaticSubtitle logical; required; default: TRUE; The quantiles values are added as subtitle to the plot.

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". A data matrix which only consists of NA, NaN, Inf, -Inf will cause a cryptical error.

Value

The function is called for its side effect.

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

boxplot.stats

Examples

      plotDistributions(cbind(rnorm(100),rnorm(100)),
             main="Random Gaussians", labels = c("N1","N2"), ylab="scale")
      plotDistributions(as.matrix(1:100), quantiles=c(0.25,0.85),
             main = "Random Gaussians", labels = c("N1"), ylab = "scale")
      plotDistributions(as.matrix(1:100), transFunc=log,
             quantiles=c(0.1,0.95), main = "Random Gaussians",
             labels = c("N1"), ylab = "scale")
           

[Package arrayMagic version 1.10.0 Index]