Maria@70: library(ape)
Maria@70: library(cluster) 
Maria@70: 
Maria@70: df = read.csv("data/cluster_freq.csv")
Maria@70: data = df[,2:dim(df)[2]]
Maria@70: rownames(data) <- df$labels
Maria@70: distMahal = as.dist(apply(data, 1, function(i) mahalanobis(data, i, cov = cov(data),tol=1e-18)))
Maria@70: hc=hclust(distMahal, method="average")
Maria@70: mypal = c("#000000", "#9B0000", "#9B0000", "#9B0000", "#9B0000")
Maria@70: clus5 = cutree(hc, 5)
Maria@70: pdf('data/hierarchical_cluster_R.pdf')
Maria@70: par(mar=c(1,1,1,1))
Maria@70: plot(as.phylo(hc),type="fan",tip.color=mypal[clus5], cex=.5, label.offset=.5)
Maria@70: dev.off()