cobramod.visualization.mapping
==============================

.. py:module:: cobramod.visualization.mapping

.. autoapi-nested-parse::

   Mapping of graph

   This modules handles the mapping of a directed graph into a matrix that can be
   used in Escher. The main function is
   :func:`cobramod.visualization.mapping.get_mapping`, which checks if the graph
   is lineal and creates the representation in a matrix. In case of cyclic path,
   it will cut it.



Functions
---------

.. autoapisummary::

   cobramod.visualization.mapping.get_graph_dict
   cobramod.visualization.mapping.get_all_values
   cobramod.visualization.mapping.child_map
   cobramod.visualization.mapping.get_index
   cobramod.visualization.mapping.unformatted_matrix
   cobramod.visualization.mapping.fill_matrix
   cobramod.visualization.mapping.format_matrix
   cobramod.visualization.mapping.get_mapping
   cobramod.visualization.mapping.transpose


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

.. py:function:: get_graph_dict(graph)

   Returns the mapping for the given graph. The mapping is defined as a list
   with a "core" path and its branches. Cyclic graphs will be cut to create
   a lineal direct graph

   .. note::
       If the first element of a branch is not in the "core", then it is
       in one of the branches.

   :returns: Mapping of the graph.
   :rtype: List

   :raises GraphKeyError: If graph is missing a value.


.. py:function:: get_all_values(dictionary, keys)

   Return a set with the all the values for a given list of keys. Elements of
   tuples will be added separately.

   :param dictionary: dictionary with keys and values
   :type dictionary: dict
   :param keys: List of keys to get values
   :type keys: list

   :returns: Values from given keys
   :rtype: Set


.. py:function:: child_map(mapping, dictionary)

   Returns the relation parent: children as a dictionary. A key represent the
   parent and the key their corresponding children

   :param mapping: Paths from given graph
   :type mapping: list
   :param dictionary: Original dictionary of directed graph.
   :type dictionary: dict

   :returns: Relation of parent and children.
   :rtype: Dict


.. py:function:: get_index(dictionary, path, value)

   Return index of item in a path, whose value is found.

   :param dictionary: Original dictionary of directed graph
   :type dictionary: dict
   :param path: A list with the name of nodes to be searched.
   :type path: list
   :param value: Value to find in path
   :type value: Any

   :returns: index of path.
   :rtype: int

   :raises Warning: If value is not found.


.. py:function:: unformatted_matrix(graph)

   Returns an unformatted matrix from a graph. The matrix represent the
   locations of the nodes and their relationships. Graph will be cut if
   cyclic. Unrelated nodes will be appended separately at the end. The matrix
   have 0 in empty positions.

   :param graph: Dictionary with relationship between nodes. A node can
                 have multiple edges, which should be presented as values.
   :type graph: dict

   Returns
       List[list]: Representation of matrix

   :raises KeyError: If keys in graph are missing


.. py:function:: fill_matrix(matrix, length)

   Fills each row of the matrix with 0 until it reaches given length

   :param matrix: Matrix to fill
   :type matrix: List[list]
   :param length: Desired length.
   :type length: int


.. py:function:: format_matrix(matrix, max_length)

   Formats given matrix and returns, if possible, a reduced matrix. Matrix
   will be filled with 0's if needed.

   :param matrix: Matrix to fill
   :type matrix: List[list]
   :param max_length: Desired length.
   :type max_length: int


.. py:function:: get_mapping(graph)

   Returns a matrix for the representation of given graph.

   :param graph: Dictionary with relationship between nodes. A node can
                 have multiple edges, which should be presented as values.
   :type graph: dict

   Returns
       List[list]: Representation of matrix

   :raises KeyError: If keys in graph are missing


.. py:function:: transpose(matrix)

   Returns a transpose matrix for given matrix.