:py:mod:`spatialtis_core.cell_interaction`
==========================================

.. py:module:: spatialtis_core.cell_interaction


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

.. py:class:: CellCombs(types: List[str], order: bool = False)

   Profile cell-cell interaction using permutation test

   :param types: All the type of cells in your research
   :param order: bool (False); If False, A->B and A<-B is the same

   .. py:method:: bootstrap(types: List[str], neighbors: spatialtis_core.types.Neighbors, labels: spatialtis_core.types.Labels, times: int = 1000, pval: float = 0.05, method: str = 'pval') -> List[Tuple[str, str, float]]

      Bootstrap functions

      1.0 means association, -1.0 means avoidance, 0.0 means insignificance.

      :param types: The type of all the cells
      :param neighbors: List of neighbors
      :param labels: List of labels
      :param times: How many times to perform bootstrap
      :param pval: The threshold of p-value
      :param method: 'pval' or 'zscore'

      :returns: List of tuples, eg.('a', 'b', 1.0), the type a and type b has a relationship as association



.. py:function:: comb_bootstrap(exp_matrix: numpy.ndarray, markers: List[str], neighbors: spatialtis_core.types.Neighbors, labels: spatialtis_core.types.Labels, pval: float = 0.05, times: int = 1000) -> List[Tuple[str, str, float]]

   Bootstrap between two types

   If you want to test co-localization between protein X and Y, first determine if the cell is X-positive
   and/or Y-positive. True is considered as positive and will be counted.

   :param exp_matrix: The expression matrix, each row should be a marker
   :param markers: Match to the row of exp_matrix
   :param neighbors: List of neighbors
   :param labels: List of labels
   :param pval: The threshold of p-value
   :param times: How many times to perform bootstrap

   :returns: The significance between markers List of (marker1, marker2, p-value)


.. py:function:: neighbor_components(neighbors: spatialtis_core.types.Neighbors, labels: spatialtis_core.types.Labels, types: List[str]) -> (List[str], List[List[int]])

   Compute the number of different cells at neighbors

   :param neighbors: The neighbors dict
   :param labels: Integer to label points
   :param types: A list of types match to points

   :returns: can be used to construct dataframe
   :rtype: (header, data)