def create_tree(nodes, edges):
outTree = Tree()
for node in nodes:
outTree.add_node(node)
for edge in edges:
outTree.add_edge(edge)
return outTree
def _initialize_tree(self, edges=None, nodes=None):
# Create Tree object
tree = Tree()
# add nodes to the tree
if nodes:
tree.add_nodes(nodes)
else:
for cluster_id, cluster in self._clustering_results.clusters.items(
):
tree.add_node(cluster.identifier, data=cluster.densities)
# TODO find clonal cluster and set it as a root
root = tree.nodes[CLONAL_CLUSTER]
tree.set_root(root)
if edges:
tree.add_edges(edges)
else:
# add edges (initially all edges are children of Clonal cluster)
for identifier, node in tree.nodes.items():
if identifier != CLONAL_CLUSTER:
tree.add_edge(root, node)
logging.debug('Tree initialized with edges {}'.format(tree.edges))
return tree
