lineage.LineageTree
===================

.. py:module:: lineage.LineageTree

.. autoapi-nested-parse::

   This file contains the LineageTree class.



Classes
-------

.. autoapisummary::

   lineage.LineageTree.LineageTree


Functions
---------

.. autoapisummary::

   lineage.LineageTree.get_Emission_Likelihoods
   lineage.LineageTree.lineage_to_tree


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

.. py:class:: LineageTree(list_of_cells, E, obs = None, states = None)

   A class for lineage trees. This class also handles algorithms for walking
   the tree to calculate various properties.


   .. py:attribute:: pi
      :type:  numpy.typing.NDArray[numpy.float64]


   .. py:attribute:: T
      :type:  numpy.typing.NDArray[numpy.float64]


   .. py:attribute:: leaves_idx
      :type:  numpy.ndarray


   .. py:attribute:: _output_lineage
      :type:  list[lineage.CellVar.CellVar] | None


   .. py:attribute:: obs
      :type:  numpy.ndarray


   .. py:attribute:: tree
      :type:  scipy.sparse.csr_array


   .. py:attribute:: states
      :type:  numpy.ndarray


   .. py:attribute:: E
      :type:  collections.abc.Sequence[lineage.states.StateDistributionGamma.StateDistribution | lineage.states.StateDistributionGaPhs.StateDistribution | lineage.states.StateDistributionCR.StateDistributionPhase]


   .. py:property:: output_lineage
      :type: list[lineage.CellVar.CellVar]


      Backwards compatibility property constructing CellVar list from arrays.



   .. py:method:: _build_cellvar_list()


   .. py:property:: non_leaves_idx
      :type: numpy.ndarray


      Return array of non-leaf cell indices.



   .. py:property:: edges
      :type: tuple[numpy.ndarray, numpy.ndarray]


      Return (parents, daughters) edge arrays.



   .. py:property:: cell_to_daughters
      :type: numpy.ndarray


      Compatibility helper returning (N, 2) array of daughter indices.



   .. py:method:: rand_init(pi, T, E, desired_num_cells, censor_condition=0, desired_experiment_time=2000000000000.0, rng=None)
      :classmethod:


      Constructor method generating pure array representation.

      :param :math:`\pi`: The initial probability matrix.
      :param T: The transition probability matrix.
      :param E: A list containing state distribution objects.
      :param desired_num_cells: The desired number of cells.
      :param censor_condition: An integer in {0, 1, 2, 3} deciding censoring type.



   .. py:method:: __len__()

      Defines the length of a lineage by returning the number of cells
      it contains.



.. py:function:: get_Emission_Likelihoods(X, E)

   Emission Likelihood (EL) matrix.

   Each element in this N by K matrix represents the probability

   :math:`P(x_n = x | z_n = k)`,

   for all :math:`x_n` and :math:`z_n` in our observed and hidden state tree
   and for all possible discrete states k.
   :param X: list of lineage trees
   :param E: The emissions likelihood
   :return: The marginal state distribution


.. py:function:: lineage_to_tree(lineage)

   Build a directed adjacency CSR array (parent -> daughter) from a lineage.