cvanmf.models
=============

.. py:module:: cvanmf.models

.. autoapi-nested-parse::

   Load existing Enterosignature models.



Attributes
----------

.. autoapisummary::

   cvanmf.models.FIVE_ES_COLORS
   cvanmf.models.logger


Classes
-------

.. autoapisummary::

   cvanmf.models.Signatures


Functions
---------

.. autoapisummary::

   cvanmf.models.five_es


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

.. py:class:: Signatures

   Bases: :py:obj:`NamedTuple`


   Definition of an existing signature model.

   This provides the definition of existing signatures required to reapply
   the signature model to new data. Where Decomposition stores the input and
   H matrix, these are not necessary for transforming new data. Rather, we
   only need the W matrix, the colors associated with each signature (for
   consistency of representation), and the preprocessing steps (to match
   features in the new data with those in the W matrix).


   .. py:method:: reapply(y: pandas.DataFrame, **kwargs) -> Decomposition

      Transform new data using this signature model.

      :param y: New data of same type as the existing model.



   .. py:attribute:: citation
      :type:  Optional[str]
      :value: None


      Citation when using this model.


   .. py:attribute:: colors
      :type:  Union[List[str], Dict[str, str]]

      Color for each signature in the model.


   .. py:attribute:: feature_match
      :type:  FeatureMatch

      Function to map features in new data to those in the model W matrix.


   .. py:attribute:: input_validation
      :type:  InputValidation

      Function to validate and potentially transform input table. Defaults
      to identity function


   .. py:attribute:: w
      :type:  pandas.DataFrame

      Feature weights (W matrix) for this model.


.. py:function:: five_es() -> Signatures

   The 5 Enterosignature model of Frioux et al.
   (2023, https://doi.org/10.1016/j.chom.2023.05.024). A summary of this model
   can also be found on the website https://enterosignatures.quadram.ac.uk.
   The `reapply` method for this model will normalise (total-sum-scale) input
   data after applying filters to match model format, so data provided does
   not need to be normalised.

   :return: 5 Enterosignature model
   :type: Signatures


.. py:data:: FIVE_ES_COLORS

.. py:data:: logger
   :type:  logging.Logger