plotColoredClusters {ClassDiscovery}R Documentation

Plot Dendrograms with Color-Coded Labels

Description

Provides an interface to plclust that makes it easier to plot dendrograms with labels that are color-coded, usually to indicate the different levels of a factor.

Usage

plotColoredClusters(hd, labs, cols, cex = 0.8, main = "", line = 0, ...)

Arguments

hd An object with S3 class hclust, as produced bny the hclust function.
labs A vector of character strings used to label the leaves inth e dendrogram
cols A vector of color names suitable for passing to the col argument of graphics routines.
cex A numeric value; the character expansion parameter of par.
main A character string; the plot title
line An integer determining how far away to plot the labels; see mtext for details.
... Any additional graphical parameters that can be supplied when plotting an hclust object.

Details

This function is used to implement the pltree methods of the Mosaic class and the PCanova class. It simply bundles a two step process (first plotting the dendrogram with no labels, followed by writing the labels in the right places with the desired colors) into a single unit.

Value

The function has no useful return value; it merely produces a plot.

See Also

plclust, hclust, Mosaic, PCanova, par

Examples

# simulate data from three different groups
d1 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
d2 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
d3 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
dd <- cbind(d1, d2, d3)

# perform hierarchical clustering using correlation
hc <- hclust(distanceMatrix(dd, 'pearson'), method='average')
cols <- rep(c('red', 'green', 'blue'), each=10)
labs <- paste('X', 1:30, sep='')

# plot the dendrogram with color-coded groups
plotColoredClusters(hc, labs=labs, cols=cols)

#cleanup
rm(d1, d2, d3, dd, hc, cols, labs)

[Package ClassDiscovery version 1.1 Index]