API
- Analyze provides analysis tools of tree samples and inference runs.
- Distances provides tree-tree distance and similarity measures.
- Interface provides dataclasses for processing MCMC data.
- Serialize contains utilities for serialization and deserialization of trees, MCMC rus and analysis.
- Tree Inference implements the mutation tree infernce; scDNA mutation profiles synthesis.
- Visualize implements visualization of trees and MCMC runs and diagostics theirof.
This package handels trees with Anytree, see our adaption in the class TreeNode below. For the inference we convert trees to binary adjacency matrices see Tree Inference, for reasons of performance.
pyggdrasil.TreeNode
Bases: Generic[NameType, DataType], NodeMixin
Tree node compatible with AnyTree. It can be annotated with the label type and the data type.
Attrs
name: identifier of the node (compatible with declared type) data: payload data parent: the node of the parent children: iterable with the children nodes
__init__(name, data=None, parent=None, children=None)
__str__()
Casts to str.
convert_anytree_to_treenode(node)
staticmethod
Converts an AnyTree node to a TreeNode.
Ignores the data attribute TreeNode nodes.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
node |
Node
|
AnyTree node to be converted |
required |
Returns: TreeNode with the same topology as the AnyTree node
convert_to_anytree_node(tree_node)
staticmethod
Converts a TreeNode to an AnyTree node.
print_topo()
Prints the topology of the tree.
pyggdrasil.compare_trees(tree1, tree2)
Compares two labeled rooted trees.
Returns:
| Type | Description |
|---|---|
bool
|
True iff the two labeled rooted trees have the same structure |
Note
Assumes that labels in each tree is unique Pyright may throw a false positive error when passing a TreeNode