Useful functions

class scHPL.utils.TreeNode(name=None, **kw)

Bases: Node

This class is an extension of Node, but with the possibility to add a classifier

Attributes:

is_binary

is_leaf

length

newick

The representation of the Node in Newick format.

Methods

ascii_art([strict, show_internal])	Return a unicode string representing a tree in ASCII art fashion.
create([name, descendants])	Create a new Node object.
get_leaf_names()	Get the names of all the leaf nodes of the subtree descending from this node.
get_leaf_names_first()	Get the names of all the leaf nodes of the subtree descending from this node.
get_leaves()	Get all the leaf nodes of the subtree descending from this node.
get_node(label)	Gets the specified node by name.
prune(leaves[, inverse])	Remove all those nodes in the specified list, or if inverse=True, remove all those nodes not in the specified list.
prune_by_names(leaf_names[, inverse])	Perform an (inverse) prune, with leaves specified by name.
remove_internal_names()	Set the name of all non-leaf nodes in the subtree to None.
remove_leaf_names()	Set the name of all leaf nodes in the subtree to None.
remove_lengths()	Set the length of all nodes in the subtree to None.
remove_names()	Set the name of all nodes in the subtree to None.
remove_redundant_nodes([preserve_lengths])	Remove all nodes which have only a single child, and attach their grandchildren to their parent.
resolve_polytomies()	Insert additional nodes with length=0 into the subtree in such a way that all non-leaf nodes have only 2 descendants, i.e. the tree becomes a fully resolved binary tree.
set_classifier(classifier)	Add a classifier to the node.
visit(visitor[, predicate])	Apply a function to matching nodes in the (sub)tree rooted at self.
walk([mode])	Traverses the (sub)tree rooted at self, yielding each visited Node.

add_descendant
get_RE
get_classifier
get_dimred
get_maxDist
get_pca
set_RE
set_dimred
set_maxDist
set_pca

classmethod create(name=None, descendants=None, **kw)

Create a new Node object.

Parameters:

• name – Node label.

• descendants – list of descendants or None.

• kw – Additonal keyword arguments are passed through to Node.__init__.

Returns:

Node instance.

get_RE()

get_classifier()

get_dimred()

get_leaf_names_first()

Get the names of all the leaf nodes of the subtree descending from this node. :return: List of names of Nodes with no descendants.

get_maxDist()

get_pca()

set_RE(maxRE)

set_classifier(classifier)

Add a classifier to the node.

set_dimred(value)

set_maxDist(maxDist)

set_pca(pca, explainingpc)

scHPL.utils.add_node(name: str, tree: TreeNode, parent: str, children: list | None = None)

Add a node to the tree manually.

Parameters:

name: String

Name of the cell population to add

tree: TreeNode

Tree the node should be added to

parent: String

Parent node the cell population should be added to. If the node should be added to the root, this should be ‘root’

children: List

If the new node is an internal node, the child nodes should also be defined. Format should be a list with strings e.g. [‘child1’, ‘child2’]

scHPL.utils.create_tree(s, strip_comments=False, **kw)

Load a list of trees from a Newick formatted string.

Parameters:

• s – Newick formatted string.

• strip_comments – Flag signaling whether to strip comments enclosed in square brackets.

• kw – Keyword arguments are passed through to Node.create.

Returns:

List of Node objects.

scHPL.utils.load(fp, strip_comments=False, **kw)

Load a list of trees from an open Newick formatted file.

Parameters:

• fp – open file handle.

• strip_comments – Flag signaling whether to strip comments enclosed in square brackets.

• kw – Keyword arguments are passed through to Node.create.

Returns:

List of Node objects.

scHPL.utils.print_tree(tree: TreeNode, new_nodes: list = [])

Print the tree

Parameters:

• tree (TreeNode) – Tree to print

• new_nodes (List = []) – Nodes recently added to the tree, these are printed in bold

Return type:

None.

scHPL.utils.read_tree(fname, encoding='utf8', strip_comments=False, **kw)

Load a list of trees from a Newick formatted file.

Parameters:

• fname – file path.

• strip_comments – Flag signaling whether to strip comments enclosed in square brackets.

• kw – Keyword arguments are passed through to Node.create.

Returns:

List of Node objects.

scHPL.utils.remove_node(name, tree: TreeNode, children: bool = True)

Remove a node from the tree

Parameters:

• name (String or List) – name of the node to remove

• tree (TreeNode) – tree containing this node

• children (Boolean = True) – if True, children are also removed. If False: children are rewired to parent node

Returns:

tree

Return type:

updated tree

scHPL.utils.rename_node(old_name, new_name: str, tree: TreeNode)

Rename a node in the tree manually.

Parameters:

old_name:

old name of the node (either a string of a list)

new_name: String

new_name of the node

tree: TreeNode

tree containing the node