Merge pull request #6 from YosefLab/add-depth

add depth

docs/api.md

@@ -2,6 +2,16 @@
 
 ## Preprocessing
 
+```{eval-rst}
+.. module:: pycea.pp
+.. currentmodule:: pycea
+
+.. autosummary::
+    :toctree: generated
+
+    pp.add_depth
+```
+
 ## Tools
 
 ```{eval-rst}

src/pycea/pl/plot_tree.py

@@ -371,7 +371,7 @@ def annotation(
     **kwargs,
 ) -> Axes:
     """\
-    Plot leaf annotations.
+    Plot leaf annotations for a tree.
 
     Parameters
     ----------

src/pycea/pp/__init__.py

@@ -0,0 +1 @@
+from .setup_tree import add_depth

src/pycea/pp/setup_tree.py

@@ -0,0 +1,39 @@
+from __future__ import annotations
+
+from collections.abc import Sequence
+
+import networkx as nx
+import treedata as td
+
+from pycea.utils import get_keyed_node_data, get_root, get_trees
+
+
+def _add_depth(tree, depth_key):
+    """Adds a depth attribute to the nodes of a tree."""
+    root = get_root(tree)
+    depths = nx.single_source_shortest_path_length(tree, root)
+    nx.set_node_attributes(tree, depths, depth_key)
+
+
+def add_depth(
+    tdata: td.TreeData, depth_key: str = "depth", tree: str | Sequence[str] | None = None, copy: bool = False
+):
+    """Adds a depth attribute to the nodes of a tree.
+
+    Parameters
+    ----------
+    tdata
+        TreeData object.
+    depth_key
+        Node attribute key to store the depth.
+    tree
+        The `obst` key or keys of the trees to use. If `None`, all trees are used.
+    copy
+        If True, returns a pd.DataFrame node depths.
+    """
+    tree_keys = tree
+    trees = get_trees(tdata, tree_keys)
+    for _, tree in trees.items():
+        _add_depth(tree, depth_key)
+    if copy:
+        return get_keyed_node_data(tdata, depth_key)

src/pycea/tl/clades.py

@@ -28,7 +28,7 @@ def _clade_name_generator():
 
 
 def _clades(tree, depth, depth_key, clades, clade_key, name_generator):
-    """Identifies clades in a tree."""
+    """Marks clades in a tree."""
     if (depth is not None) and (clades is None):
         nodes = _nodes_at_depth(tree, get_root(tree), [], depth, depth_key)
         clades = dict(zip(nodes, name_generator))
@@ -61,7 +61,7 @@ def clades(
     tree: str | Sequence[str] | None = None,
     copy: bool = False,
 ) -> None | Mapping:
-    """Identifies clades in a tree.
+    """Marks clades in a tree.
 
     Parameters
     ----------

src/pycea/tl/sort.py

@@ -14,14 +14,17 @@ def _sort_tree(tree, key, reverse=False):
             try:
                 sorted_children = sorted(tree.successors(node), key=lambda x: tree.nodes[x][key], reverse=reverse)
             except KeyError as err:
-                raise KeyError(f"Node {next(tree.successors(node))} does not have a {key} attribute.") from err
+                raise KeyError(
+                    f"Node {next(tree.successors(node))} does not have a {key} attribute.",
+                    "You may need to call `ancestral_states` to infer internal node values",
+                ) from err
             tree.remove_edges_from([(node, child) for child in tree.successors(node)])
             tree.add_edges_from([(node, child) for child in sorted_children])
     return tree
 
 
 def sort(tdata: td.TreeData, key: str, reverse: bool = False, tree: str | Sequence[str] | None = None) -> None:
-    """Reorders branches based on a given key.
+    """Reorders branches based on a node attribute.
 
     Parameters
     ----------

tests/test_setup_tree.py

@@ -0,0 +1,26 @@
+import networkx as nx
+import pandas as pd
+import pytest
+import treedata as td
+
+from pycea.pp.setup_tree import add_depth
+
+
+@pytest.fixture
+def tdata():
+    tree1 = nx.DiGraph([("root", "A"), ("root", "B"), ("B", "C"), ("B", "D")])
+    tree2 = nx.DiGraph([("root", "E"), ("root", "F")])
+    tdata = td.TreeData(obs=pd.DataFrame(index=["A", "C", "D", "E", "F"]), obst={"tree1": tree1, "tree2": tree2})
+    yield tdata
+
+
+def test_add_depth(tdata):
+    depths = add_depth(tdata, depth_key="depth", copy=True)
+    assert depths.loc[("tree1", "root"), "depth"] == 0
+    assert depths.loc[("tree1", "C"), "depth"] == 2
+    assert tdata.obst["tree1"].nodes["root"]["depth"] == 0
+    assert tdata.obst["tree1"].nodes["C"]["depth"] == 2
+
+
+if __name__ == "__main__":
+    pytest.main(["-v", __file__])