:py:mod:`evomap.transform`
==========================

.. py:module:: evomap.transform

.. autoapi-nested-parse::

   Useful transformations after maps have been generated.



Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   evomap.transform.align_maps
   evomap.transform.align_map
   evomap.transform.PCA
   evomap.transform.rotate_map
   evomap.transform.rotate_maps



.. py:function:: align_maps(Xs, X_ref)

   Align a sequence of maps to a reference map via Orthogonal
   Procrustes Analysis.

   :param Xs: List of map coordinates
   :type Xs: list of ndarrays, each of shape (n_samples, n_dims)
   :param X_ref: Reference map to which all other maps should be aligned to
   :type X_ref: ndarray, shape (n_samples, n_dims)

   :returns: List of aligned map coordinates
   :rtype: list of ndarrays, each of shape (n_samples, n_dims)


.. py:function:: align_map(X, X_ref)

   Align a map to a reference map via Orthogonal Procrustes Analysis.

   :param X: Map coordinates
   :type X: ndarray of shape (n_samples, n_dims)
   :param X_ref: Reference map
   :type X_ref: ndarray of shape (n_samples, n_dims)

   :returns: Aligned map
   :rtype: ndarray, of shape (n_samples, n_dims)


.. py:function:: PCA(X, num_components)


.. py:function:: rotate_map(Y_2D)


.. py:function:: rotate_maps(Y, inclusions)

   Rotate a map (or sequence of maps) such that the x-axis corresponds to
   the direction of maximum variance.

   :param Y: _description_
   :type Y: _type_