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meren/for_tom.R

Created August 24, 2013 00:12
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This should create an iTOL compatible newick tree under your home directory..
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for_tom.R
library('ape')
library('vegan')
library('ade4')
raw_data <- t(data.matrix(read.table('YOUR TAB DELIMITED TRANSCRIPTOMIC DATA MATRIX', header = TRUE, row.names = 1, sep="\t")))
drows<-vegdist(t(raw_data), method='euclidean', na.rm=TRUE)
hc <- hclust(drows, method='ward')
phy <- hclust2phylog(hc, add.tools = TRUE)
write.tree(as.phylo(phy), file="~/newick.tre")
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