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diff scripts_R/radial_dendro.R @ 70:cc028157502a branch-tests

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scripts R
author Maria Panteli
date Fri, 22 Sep 2017 16:29:32 +0100
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts_R/radial_dendro.R	Fri Sep 22 16:29:32 2017 +0100
@@ -0,0 +1,14 @@
+library(ape)
+library(cluster) 
+
+df = read.csv("data/cluster_freq.csv")
+data = df[,2:dim(df)[2]]
+rownames(data) <- df$labels
+distMahal = as.dist(apply(data, 1, function(i) mahalanobis(data, i, cov = cov(data),tol=1e-18)))
+hc=hclust(distMahal, method="average")
+mypal = c("#000000", "#9B0000", "#9B0000", "#9B0000", "#9B0000")
+clus5 = cutree(hc, 5)
+pdf('data/hierarchical_cluster_R.pdf')
+par(mar=c(1,1,1,1))
+plot(as.phylo(hc),type="fan",tip.color=mypal[clus5], cex=.5, label.offset=.5)
+dev.off()