scPhyloX.simulation.haematopoiesis
==================================

.. py:module:: scPhyloX.simulation.haematopoiesis


Classes
-------

.. autoapisummary::

   scPhyloX.simulation.haematopoiesis.Reaction
   scPhyloX.simulation.haematopoiesis.Cell
   scPhyloX.simulation.haematopoiesis.System


Functions
---------

.. autoapisummary::

   scPhyloX.simulation.haematopoiesis.bt
   scPhyloX.simulation.haematopoiesis.simulation


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

.. py:function:: bt(t, a, b, k, t0)

.. py:class:: Reaction(rate=0.0, num_lefts=None, num_rights=None, index=None)

   Cell division/differentiation type

   Args:
       rate:
           reaction rate function
       num_lefts:
           Cell numbers before reaction
       num_right:
           Cell numbers after reaction
       index:
           Reaction index


   .. py:attribute:: rate
      :value: 0.0



   .. py:attribute:: num_lefts


   .. py:attribute:: num_rights


   .. py:attribute:: num_diff


   .. py:attribute:: index
      :value: None



   .. py:method:: combine(n, s)


   .. py:method:: propensity(n, t)


.. py:class:: Cell(seq=None, gen=None, cellid=None, celltype=None, is_alive=True, lseq=1500, init=False)

   Cell class

   Args:
       seq:
           DNA sequence
       gen: 
           Cell generation
       cellid: 
           Cell id
       celltype:
           Cell type, stem/non-stem cell
       is_alive: 
           Is cell alive or died
       lseq: 
           Length of DNA seq 
       init: 
           if init, cell will generate DNA seq with given length lseq automatically


   .. py:attribute:: seq
      :value: None



   .. py:attribute:: gen
      :value: None



   .. py:attribute:: celltype
      :value: None



   .. py:attribute:: lseq
      :value: 1500



   .. py:attribute:: cellid
      :value: None



   .. py:attribute:: is_alive
      :value: True



   .. py:method:: initialize(lseq)

      Generate DNA seq with given length lseq



.. py:class:: System(num_elements, inits=None, nbase=1500, mut_rate=1, max_t=35, start_t=0)

   Gillespie simulation

   Args:
       num_elements: 
           Cell type number
       inits: 
           Initial cell number
       nbase:
           length of cell DNA seq
       mut_rate:
           mutation rate of DNA seq, follows Poisson distribution
       max_t:
           maximum simulation time
       start_t:
           Mutate start time


   .. py:attribute:: num_elements


   .. py:attribute:: reactions
      :value: []



   .. py:attribute:: start_t
      :value: 0



   .. py:attribute:: max_t
      :value: 35



   .. py:attribute:: mut_rate
      :value: 1



   .. py:attribute:: global_id


   .. py:attribute:: Stemcells


   .. py:attribute:: Diffcells


   .. py:attribute:: mut_num
      :value: 0



   .. py:attribute:: cell_num


   .. py:attribute:: mut_time
      :value: []



   .. py:attribute:: mut_num_SC


   .. py:attribute:: mut_num_DC


   .. py:attribute:: log_cells


   .. py:attribute:: lineage_info


   .. py:method:: add_reaction(rate=0.0, num_lefts=None, num_rights=None, index=None)

      Add reactions to simulation

      Args:
          rate:
              reaction rate function
          num_lefts:
              Cell numbers before reaction
          num_right:
              Cell numbers after reaction
          index:
              Reaction index



   .. py:method:: mutate(cell, mutrate)

      simulation DNA mutation

      Args:
          cell:
              cell
          mutrate:
              mutation rate
      Return:
          cell:
              cell with mutated DNA seq



   .. py:method:: stemrenewal()

      stem cell -> 2 stem cells



   .. py:method:: diffrenewal()

      diff cell -> 2 diff cells



   .. py:method:: stemdiff()

      stem cell -> non-stem cell + non-stem cell



   .. py:method:: diffdeath()

      non-stem cell -> death cell



   .. py:method:: stemasym()

      stem cell -> stem cell + non-stem cell



   .. py:method:: evolute(steps)


.. py:function:: simulation(x0, max_t, mut_rate, a, b, p, r, k, t0, r1, b1)

   Run gillespie simulation in tissue development model

   Args:
       x0:
           initial cell number
       max_t:
           stop time
       mut_rate:
           mutation rate
       a,b,p,r,k,d,t0:
           paras
   Return:
       Object:
           gillespie simulator with results