Save dendrogram to newick format

Question

如何将scipy生成的树形图保存为Newick格式 ？

Answer 1

You need the linkage matrix Z, which is the input to the scipy dendrogram function, and convert that to Newick format. Additionally, you need a list 'leaf_names' with the names of your leaves. Here is a function that will do the job:

from scipy.cluster import hierarchy
def getNewick(node, newick, parentdist, leaf_names):
    if node.is_leaf():
        return "%s:%.2f%s" % (leaf_names[node.id], parentdist - node.dist, newick)
    else:
        if len(newick) > 0:
            newick = "):%.2f%s" % (parentdist - node.dist, newick)
        else:
            newick = ");"
        newick = getNewick(node.get_left(), newick, node.dist, leaf_names)
        newick = getNewick(node.get_right(), ",%s" % (newick), node.dist, leaf_names)
        newick = "(%s" % (newick)
        return newick

tree = hierarchy.to_tree(Z,False)
getNewick(tree, "", tree.dist, leaf_names)