Cluster.R

Code snipits and programs written in R, S or S-PLUS clusterPlot <- function(x, rowNames = NULL, dmethod = "euclidian", hmethod="complete", ...) {

 oldpar <- par(mfrow=c(2,1))  

 if(is.character(rowNames) & (length(rowNames) == nrow(x))) {
   rownames(x) <- rowNames
 }
 xDist <- dist(x, method=dmethod)
 

1. 1) Tree dendrogram

 xClust <- hclust(xDist, method=hmethod)
 plclust(xClust, sub="")
 

1. 2) Image plot...

 image(x = 1:nrow(x), y = 1:ncol(x), z = x[xClust$order, ], col=heat.colors(nrow(x)), ...)
 par(oldpar)
 invisible()

}

1. Euclidian distance

X <- matrix(1:9, nc=3) X1 <- X[1,] X2 <- X[2,]

dist(X) sqrt(sum((X1-X2)^2))

1. Example

x <- matrix(rnorm(40), nc=4) colnames(x) <- LETTERS[1:4] rownames(x) <- letters[1:10] clusterPlot(x) clusterPlot(x, rowNames = LETTERS[1:10])