25.3 Cluster analysis

kmd <- read.table("c:\\temp\\kmeansdata.txt",header=T)
attach(kmd)

names(kmd)

par(mfrow=c(2,2))

plot(x,y,pch=16)

plot(x,y,col=group,pch=16)
model <- kmeans(data.frame(x,y),6)
plot(x,y,col=model[[1]])
model <- kmeans(data.frame(x,y),4)
plot(x,y,col=model[[1]])

par(mfrow=c(1,1))

model <- kmeans(data.frame(x,y),6)

table(model[[1]],group)

taxa <- read.table("c:\\temp\\taxon.txt",header=T)

attach(taxa)

names(taxa)

kmeans(taxa,4)

pgdata <- read.table("c:\\temp\\pgfull.txt",header=T)
attach(pgdata)

labels <- paste(plot,letters[lime],sep="")

hpg <- hclust(dist(pgdata[,1:54]))

plot(hpg,labels=labels,main= "") 

plot(hclust(dist(taxa)),main="")