Scipy Interoperability functions

binary_hierarchy_to_scipy_linkage_matrix(tree)

Converts an Higra binary hierarchy to a SciPy linkage matrix.

scipy_linkage_matrix_to_binary_hierarchy(...)

Converts a SciPy linkage matrix to an Higra binary hierarchy.
binary_hierarchy_to_scipy_linkage_matrix(tree, altitudes=None, area=None)[source]

Converts an Higra binary hierarchy to a SciPy linkage matrix.

From SciPy documentation:

An \(n-1\) by 4 matrix \(Z\) is returned. At the \(i\)-th iteration, clusters with indices \(Z[i, 0]\) and \(Z[i, 1]\) are combined to form cluster \(n+i\). A cluster with an index less than \(n\) corresponds to one of the \(n\) original observations. The distance between clusters \(Z[i, 0]\) and \(Z[i, 1]\) is given by \(Z[i, 2]\). The fourth value \(Z[i, 3]\) represents the number of original observations in the newly formed cluster.

If altitudes is not specified, the value provided by attribute_regular_altitudes() on tree is used.

If area is not specified, the value provided by attribute_area() on tree is used.

Parameters:

  • tree – Input tree

  • altitudes – Tree nodes altitudes (should be increasing w.r.t tree)

  • area – Tree nodes area (should be increasing w.r.t tree)

Returns:

A linkage matrix

scipy_linkage_matrix_to_binary_hierarchy(linkage_matrix)[source]

Converts a SciPy linkage matrix to an Higra binary hierarchy.

The result is composed of

  • a tree

  • an array containing the altitudes of the tree nodes

  • an array containing the area of the tree nodes

Parameters:

linkage_matrix – a 2d array as produced by the linkage method of SciPy

Returns:

a tuple (tree, altitudes, area)