[英]Save dendrogram to newick format
您需要链接矩阵Z,它是scipy树形图函数的输入,并将其转换为Newick格式。 此外,您需要一个带有叶子名称的“leaf_names”列表。 这是一个可以完成工作的功能:
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)
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