repic.commands.get_cliques
==========================

.. py:module:: repic.commands.get_cliques

.. autoapi-nested-parse::

   Finds cliques (potential consensus particles) of size k in each graph (micrograph)



Attributes
----------

.. autoapisummary::

   repic.commands.get_cliques.name
   repic.commands.get_cliques.parser


Functions
---------

.. autoapisummary::

   repic.commands.get_cliques.add_arguments
   repic.commands.get_cliques.add_nodes_to_graph
   repic.commands.get_cliques.calc_jaccard
   repic.commands.get_cliques.find_cliques
   repic.commands.get_cliques.main


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

.. py:data:: name
   :value: 'get_cliques'


   module name (used by argparse subparser)

   :type: str

.. py:function:: add_arguments(parser)

   Adds argparse command line arguments for get_cliques.py

   :param parser: argparse parse_args() object
   :type parser: object

   :returns: None


.. py:function:: add_nodes_to_graph(graph, node_pairs, node_names, k=3)

   Adds vertices and edges to the graph

   :param graph: NetworkX graph() object
   :type graph: obj
   :param node_pairs: list of paired vertex (particle bounding box) coordinates and their edge weight
   :type node_pairs: list
   :param node_names: list of node (particle picking algorithm) names
   :type node_names: list

   :keyword k: number of methods
   :kwtype k: int, default=3

   :returns: None


.. py:function:: calc_jaccard(x, y, a, b, box_size)

   Calculates Jaccard Index (similarity) for particle bounding boxes A (x,y) and B (a,b) with given box size

   :param x: x-coodinate of particle bounding box A
   :type x: int
   :param y: y-coordinate of particle bounding box A
   :type y: int
   :param a: x-coordinate of particle bounding box B
   :type a: int
   :param b: y-coordinate of particle bounding box B
   :type b: int
   :param box_size: particle bounding box height/width
   :type box_size: int

   :returns: Jaccard Index of two particle bounding boxes
   :rtype: float


.. py:function:: find_cliques(graph, k)

   Finds all cliques in graph of size k

   :param graph: NetworkX graph() object
   :type graph: obj
   :param k: clique size
   :type k: int

   :returns: set of k-sized cliques in the graph
   :rtype: set


.. py:function:: main(args)

   Builds NetworkX graph from file set and finds all k-sized cliques

   :param args: argparse command line argument object
   :type args: obj


.. py:data:: parser

   argparse parse_args() object

   :type: obj