Mercurial > hg > plosone_underreview
annotate scripts_R/radial_dendro.R @ 76:d17833be50ca branch-tests
merged
| author | Maria Panteli <m.x.panteli@gmail.com> |
|---|---|
| date | Fri, 22 Sep 2017 16:30:36 +0100 |
| parents | cc028157502a |
| children |
| rev | line source |
|---|---|
| Maria@70 | 1 library(ape) |
| Maria@70 | 2 library(cluster) |
| Maria@70 | 3 |
| Maria@70 | 4 df = read.csv("data/cluster_freq.csv") |
| Maria@70 | 5 data = df[,2:dim(df)[2]] |
| Maria@70 | 6 rownames(data) <- df$labels |
| Maria@70 | 7 distMahal = as.dist(apply(data, 1, function(i) mahalanobis(data, i, cov = cov(data),tol=1e-18))) |
| Maria@70 | 8 hc=hclust(distMahal, method="average") |
| Maria@70 | 9 mypal = c("#000000", "#9B0000", "#9B0000", "#9B0000", "#9B0000") |
| Maria@70 | 10 clus5 = cutree(hc, 5) |
| Maria@70 | 11 pdf('data/hierarchical_cluster_R.pdf') |
| Maria@70 | 12 par(mar=c(1,1,1,1)) |
| Maria@70 | 13 plot(as.phylo(hc),type="fan",tip.color=mypal[clus5], cex=.5, label.offset=.5) |
| Maria@70 | 14 dev.off() |