clustering_utils
================

.. py:module:: clustering_utils


Functions
---------

.. autoapisummary::

   clustering_utils.clustering_of_correlation_matrix
   clustering_utils.plot_dendrogram


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

.. py:function:: clustering_of_correlation_matrix(correlation_matrix: numpy.typing.NDArray[numpy.float64], reactions: List, linkage: str = 'ward', t: float = 4.0, correction: bool = True) -> Tuple[numpy.typing.NDArray[numpy.float64], numpy.typing.NDArray[numpy.float64], List[List]]

   Function for hierarchical clustering of the correlation matrix

   Keyword arguments:
   correlation_matrix (NDArray[np.float64]) -- A numpy 2D array of a correlation matrix
   reactions (List) -- A list with the corresponding reactions (must be in accordance with the correlation matrix)
   linkage (str) -- linkage defines the type of linkage. Available linkage types are: single, average, complete, ward.
   t (float) -- A threshold that defines a threshold that cuts the dendrogram at a specific height and produces clusters
   correction (bool) -- A boolean variable that if True converts the values of the the correlation matrix to absolute values.
                        
   Returns:
   Tuple[NDArray[np.float64], NDArray[np.float64], List[List]]
       dissimilarity_matrix (NDArray[np.float64]) -- The dissimilarity matrix calculated from the given correlation matrix
       labels (NDArray[np.float64]) -- Integer labels corresponding to clusters
       clusters (List[List]) -- Nested list containing reaction IDs grouped based on their cluster labels


.. py:function:: plot_dendrogram(dissimilarity_matrix: numpy.typing.NDArray[numpy.float64], reactions: List, group_map: dict, linkage: str = 'ward', t: float = 4.0, label_fontsize: int = 10, height: int = 600, width: int = 1000, show_labels: bool = True, title: str = '')

   Function that plots the dendrogram from hierarchical clustering

   Keyword arguments:
   dissimilarity_matrix (NDArray[np.float64]) -- The dissimilarity matrix calculated from the `clustering_of_correlation_matrix` function
   reactions (List) -- List with reactions IDs
   group_map (Dict) -- Dictionary mapping reactions to pathways
   linkage (str) -- linkage defines the type of linkage. Available linkage types are: single, average, complete, ward.
   t (float) -- A threshold that defines a threshold that cuts the dendrogram at a specific height
   label_fontsize (int) -- Size for the plotted labels (reaction IDs)
   height (int) -- Defines the height of the plot
   width (int) -- Defines the width of the plot
   show_labels (bool) -- Boolean variable that if True labels are shown in the x-axis
   title (str) -- Title for the plot