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analysis.tree_hierarchy

merge_func​

def merge_func(transition_matrix: np.ndarray, n_clusters: int,
               motif_norm: np.ndarray,
               merge_sel: int) -> Tuple[np.ndarray, np.ndarray]

Merge nodes in a graph based on a selection criterion.

Parameters

  • transition_matrix (np.ndarray): The transition matrix of the graph.
  • n_clusters (int): The number of clusters.
  • motif_norm (np.ndarray): The normalized motif matrix.
  • merge_sel (int): The merge selection criterion.
  • 0: Merge nodes with highest transition probability.
  • 1: Merge nodes with lowest cost.

Returns

  • Tuple[np.ndarray, np.ndarray]: A tuple containing the merged nodes.

graph_to_tree​

def graph_to_tree(motif_usage: np.ndarray,
                  transition_matrix: np.ndarray,
                  n_clusters: int,
                  merge_sel: int = 1) -> nx.Graph

Convert a graph to a tree.

Parameters

  • motif_usage (np.ndarray): The motif usage matrix.
  • transition_matrix (np.ndarray): The transition matrix of the graph.
  • n_clusters (int): The number of clusters.
  • merge_sel (int, optional): The merge selection criterion. Defaults to 1.
  • 0: Merge nodes with highest transition probability.
  • 1: Merge nodes with lowest cost.

Returns

  • nx.Graph: The tree.

_traverse_tree_cutline​

def _traverse_tree_cutline(
        T: nx.Graph,
        node: List[str],
        traverse_list: List[str],
        cutline: int,
        level: int,
        community_bag: List[List[str]],
        community_list: List[str] | None = None) -> List[List[str]]

DEPRECATED in favor of bag_nodes_by_cutline. Helper function for tree traversal with a cutline.

Parameters

  • T (nx.Graph): The tree to be traversed.
  • node (List[str]): Current node being traversed.
  • traverse_list (List[str]): List of traversed nodes.
  • cutline (int): The cutline level.
  • level (int): The current level in the tree.
  • community_bag (List[List[str]]): List of community bags.
  • community_list (List[str], optional): List of nodes in the current community bag.

Returns

  • List[List[str]]: List of lists community bags.

traverse_tree_cutline​

def traverse_tree_cutline(T: nx.Graph,
                          root_node: str | None = None,
                          cutline: int = 2) -> List[List[str]]

DEPRECATED in favor of bag_nodes_by_cutline. Traverse a tree with a cutline and return the community bags.

Parameters

  • T (nx.Graph): The tree to be traversed.
  • root_node (str, optional): The root node of the tree. If None, traversal starts from the root.
  • cutline (int, optional): The cutline level.

Returns

  • List[List[str]]: List of community bags.

bag_nodes_by_cutline​

def bag_nodes_by_cutline(tree: nx.Graph, cutline: int = 2, root: str = "Root")

Bag nodes of a tree by a cutline.

Parameters

  • tree (nx.Graph): The tree to be bagged.
  • cutline (int, optional): The cutline level. Defaults to 2.
  • root (str, optional): The root node of the tree. Defaults to 'Root'.

Returns

  • List[List[str]]: List of bags of nodes.