gneiss.util.match_tips¶

gneiss.util.match_tips(table, tree)[source]¶

Returns the contingency table and tree with matched tips.

Sorts the columns of the contingency table to match the tips in the tree. The ordering of the tips is in post-traversal order.

If the tree is multi-furcating, then the tree is reduced to a bifurcating tree by randomly inserting internal nodes.

The intersection of samples in the contingency table and the tree will returned.

Parameters:

table (pd.DataFrame) – Contingency table where samples correspond to rows and features correspond to columns.
tree (skbio.TreeNode) – Tree object where the leafs correspond to the features.

Returns:

pd.DataFrame – Subset of the original contingency table with the common features.
skbio.TreeNode – Sub-tree with the common features.

Raises:

ValueError: – Raised if table and tree have incompatible sizes.