:py:mod:`evomap.mapping`
========================

.. py:module:: evomap.mapping


Subpackages
-----------
.. toctree::
   :titlesonly:
   :maxdepth: 3

   evomap/index.rst


Submodules
----------
.. toctree::
   :titlesonly:
   :maxdepth: 1

   _cmds/index.rst
   _mds/index.rst
   _optim/index.rst
   _sammon/index.rst
   _tsne/index.rst


Package Contents
----------------

Classes
~~~~~~~

.. autoapisummary::

   evomap.mapping.CMDS
   evomap.mapping.EvoMDS
   evomap.mapping.EvoSammon
   evomap.mapping.EvoTSNE
   evomap.mapping.Sammon
   evomap.mapping.TSNE
   evomap.mapping.MDS




.. py:class:: CMDS(n_dims=2)


   .. py:method:: _cmdscale(D, n_dims)
      :staticmethod:

      Classical multidimensional scaling (MDS)

      :param D: Symmetric distance matrix.
      :type D: (n, n) array

      :returns: * **Y** (*(n, p) array*) -- Configuration matrix. Each column represents a dimension. Only the
                  p dimensions corresponding to positive eigenvalues of B are returned.
                  Note that each dimension is only determined up to an overall sign,
                  corresponding to a reflection.
                * **e** (*(n,) array*) -- Eigenvalues of B.


   .. py:method:: fit(X)


   .. py:method:: fit_transform(X)



.. py:class:: EvoMDS(alpha=0, p=1, n_dims=2, n_iter=2000, n_iter_check=50, init=None, mds_type='absolute', verbose=0, input_type='distance', max_halves=5, tol=0.001, n_inits=1, step_size=1, max_tries=5)


   Bases: :py:obj:`evomap.mapping.evomap._core.EvoMap`

   EvoMap Interface. Implements default functions shared by all
   implementation in its child classes.

   .. py:method:: fit(Xs, inclusions=None)


   .. py:method:: fit_transform(Xs, inclusions=None)



.. py:class:: EvoSammon(alpha=0, p=1, n_dims=2, n_iter=2000, n_iter_check=50, init=None, verbose=0, input_type='distance', max_halves=5, tol=0.001, n_inits=1, step_size=1, max_tries=5)


   Bases: :py:obj:`evomap.mapping.evomap._core.EvoMap`

   EvoMap Interface. Implements default functions shared by all
   implementation in its child classes.

   .. py:method:: fit(Xs, inclusions=None)


   .. py:method:: fit_transform(Xs, inclusions=None)



.. py:class:: EvoTSNE(alpha=0, p=1, n_dims=2, perplexity=15, stop_lying_iter=250, early_exaggeration=4, eta='auto', initial_momentum=0.5, final_momentum=0.8, n_iter=2000, n_iter_check=50, init=None, verbose=0, input_type='distance', max_halves=5, tol=0.001, n_inits=1, max_tries=5)


   Bases: :py:obj:`evomap.mapping.evomap._core.EvoMap`

   EvoMap Interface. Implements default functions shared by all
   implementation in its child classes.

   .. py:method:: fit(Xs, inclusions=None)


   .. py:method:: fit_transform(Xs, inclusions=None)



.. py:class:: Sammon(n_dims=2, n_iter=2000, n_iter_check=50, init=None, verbose=0, input_type='distance', max_halves=5, tol=0.001, n_inits=1, step_size=1)


   .. py:method:: fit(X)


   .. py:method:: fit_transform(X)



.. py:class:: TSNE(n_dims=2, perplexity=15, n_iter=2000, stop_lying_iter=250, early_exaggeration=4, initial_momentum=0.5, final_momentum=0.8, eta='auto', n_iter_check=50, init=None, verbose=0, input_type='distance', max_halves=5, tol=0.001, n_inits=1, step_size=1)


   .. py:method:: fit(X)


   .. py:method:: fit_transform(X)



.. py:class:: MDS(n_dims=2, mds_type=None, n_iter=2000, n_iter_check=50, init=None, verbose=0, input_type='distance', max_halves=5, tol=0.001, n_inits=1, step_size=1)


   .. py:method:: fit(X)


   .. py:method:: fit_transform(X)