Comments (1)
you can use hierarchical clustering, following as.phylo
to convert it to phylo
tree object. You can also save the tree to newick format using write.tree
.
> require(ape)
> d=matrix(abs(rnorm(100)), nrow=10)
> rownames(d) = paste0("g", 1:10)
> colnames(d) = paste0("t", 1:10)
> tre = d %>% as.dist %>% hclust %>% as.phylo
> tre
Phylogenetic tree with 10 tips and 9 internal nodes.
Tip labels:
g1, g2, g3, g4, g5, g6, ...
Rooted; includes branch lengths.
> tmpfile = tempfile()
> write.tree(tre, file=tmpfile)
> readLines(tmpfile)
[1] "(((g10:0.08570056643,(g2:0.04299505849,g5:0.04299505849):0.04270550794):0.6898330804,(g1:0.1623773693,g6:0.1623773693):0.6131562775):0.6264608697,((g4:0.01327553131,g9:0.01327553131):0.8007602439,(g7:0.0942671152,(g3:0.03158512824,g8:0.03158512824):0.06268198696):0.71976866):0.5879587413);"
from ggtree.
Related Issues (20)
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from ggtree.