plot.imageMatrix {arrayMagic}R Documentation

Visualisation of a matrix

Description

Visualisation of a data matrix, e.g. a matrix representing a two dimensional area, a matrix of distance or similarity scores, or any numeric matrix. Coloured boxes represent values, labels will be drawn inside the box.

Usage

plot.imageMatrix(x, labelMatrix, zlim, separateZScale=FALSE, zScale=TRUE, colourRamp, reverseYaxis = TRUE, labels, xLabels, yLabels, width=8, height=7, labelMatrixTextScaling=0.7, plotOutput="standard", fileName, ...)

Arguments

x data matrix, class matrix; required; default missing
labelMatrix matrix of labels of class array of dim(x); optional; default missing
zlim numeric vector; defines the maximal z-range of the plot; default missing
zScale logical; adds a scale to the plot; required; default TRUE
separateZScale logical; extra plot of the scale; required; default FALSE
colourRamp vector of colours; optional; default missing
reverseYaxis logical; required; default TRUE
labels vector of names corresponding to a quadratic x; optional; default missing
xLabels vector of names corresponding to the columns of x overrides labels; optional; default missing
yLabels vector of names corresponding to the rows of x overrides labels; optional; default missing
width graphics window width; required; default: 8
height graphics window height; required; default: 7
labelMatrixTextScaling numeric; required; default: 0.7
plotOutput character string specifying either "standard", "screen", "twoScreens", "pdf" or "win.metafile"; required; default: "standard"
fileName character string specifying the file path and file name; optional; default missing
... arguments are passed to image(), for example xlab, ylab (x- and y-axis label) and main (plot title)

Details

If no labels are supplied, the dimnames of x or if missing a simple numbering is used instead.

Author(s)

Andreas Buness <a.buness@dkfz.de>

Examples


 plot.imageMatrix(x=matrix(c(3,4,4,3),nrow=2, ncol=2),labels=c("one","two"))
 ma <- matrix(c(0.3,0.01,0.7,0.1,0.5,0.3,1,0.5,01), nrow=3,ncol=3)
 class(ma) <- c("imageMatrix", "matrix")
 plot(ma, labelMatrix=ma,labels=c("one","two", "three"), zlim=c(0,1))
 ma <- matrix(c(0.3, 0.01, 0.7, 0.1, 0.5, 0.3, 1, 0.5, 1, 0, 1, 0), nrow = 4, ncol = 3, byrow=TRUE )
 class(ma) <- c("imageMatrix", "matrix")
 plot(ma, labelMatrix = ma, xLabels = c("one", "two", "three"), zlim=c(0,1))
 plot(ma, reverseYaxis=FALSE, labelMatrix = ma, xLabels = c("one", "two", "three"), zlim=c(0,1))



 

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