phylovelo.gene_expr
===================

.. py:module:: phylovelo.gene_expr


Classes
-------

.. autoapisummary::

   phylovelo.gene_expr.Gene
   phylovelo.gene_expr.GeneExpr


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

.. py:class:: Gene(mu0: float, drift: float, sigma: float = None, t0: int = 0)

   Gene class

   Args:
       mu0:
           Initial expression
       drift:
           Drift coefficient of DP
       sigma:
           Diffusion coefficient of DP
       t0:
           Gene initial time


   .. py:attribute:: mu0


   .. py:attribute:: drift


   .. py:attribute:: t0
      :value: 0



   .. py:attribute:: base_expr


   .. py:method:: diffusion()

      Diffusion one step.



   .. py:method:: base_expr_calc(t: int)

      Calculate base expression

      Args
          t:
              time
      Return:
          Base expression at time t



.. py:class:: GeneExpr(Ngene: int, r_variant_gene: float, diff_map: dict, state_time: dict, forward_map: dict = None)

   Gene expression program

   Args:
       Ngene:
           Gene number
       r_variant_gene:
           Ratio of gene changes with differentiation
       diff_map:
           Differentiation relationships between different cell types
           {a:[b,c]} means 'a' is differentiated from 'b' and 'c'
       state_time:
           Pseudo time of each states
       forward_map:
           Only use in convergent model simulation
           {a:b} means 'a' will differentiated to 'b'


   .. py:attribute:: Ngene


   .. py:attribute:: Nstates


   .. py:attribute:: variant_gene


   .. py:attribute:: expr_rec


   .. py:attribute:: cells_genetype


   .. py:attribute:: diff_map


   .. py:attribute:: state_time


   .. py:attribute:: forward_map
      :value: None



   .. py:method:: generate_genes(mu0_loc: float = 20, mu0_scale: float = 3, drift_loc: float = 0, drift_scale: float = 1)

      Generate genes

      Args:
          mu0_loc:
              Mean of initial expression
          mu0_scale:
              Variation of initial expression
          drift_loc:
              Mean of gene drift
          drift_scale:
              Variation of drift



   .. py:method:: expr(state, time)