scPhyloX.tools.data_factory
===========================

.. py:module:: scPhyloX.tools.data_factory


Attributes
----------

.. autoapisummary::

   scPhyloX.tools.data_factory.population_size
   scPhyloX.tools.data_factory.tumor_data
   scPhyloX.tools.data_factory.tumor_size


Functions
---------

.. autoapisummary::

   scPhyloX.tools.data_factory.cell_number_calc
   scPhyloX.tools.data_factory.get_branchlen
   scPhyloX.tools.data_factory.get_mutnum
   scPhyloX.tools.data_factory.mutnum_fly
   scPhyloX.tools.data_factory.branchlen_fly


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

.. py:data:: population_size

.. py:function:: cell_number_calc(w, l, r, coef=100000000.0)

   Calculate tumor cell number with given width, height and scale

   Args:
       w: 
           width
       l:
           heigth
       r:
           scale
       coef:
           cell density
   Return:
       float:
           cell number


.. py:data:: tumor_data

.. py:data:: tumor_size

.. py:function:: get_branchlen(seqtab: numpy.ndarray = None, sys=None)

   Calculate LP distance with given mutation character matrix

   Args:
       seqtab:
           mutation character matrix
       sys:
           Gillespie simulator with results
   Return:
       np.array:
           LP distance 


.. py:function:: get_mutnum(seqtab=None, sys=None, filter_trunk=True)

   Calculate LR distance with given mutation character matrix

   Args:
       seqtab:
           mutation character matrix
       sys:
           Gillespie simulator with results
       filter_trunk:
           Filter trunk mutations
   Return:
       np.array:
           LR distance 


.. py:function:: mutnum_fly(seqs, ref)

   calculate LR distance for SMALT-fly dataset

   Args:
       seqs:
           DNA muataion character matrix
       ref:
           reference seuence

   Return:
       np.array:
           LR distance 


.. py:function:: branchlen_fly(seqs, ref, rs=1)

   calculate LP distance for SMALT-fly dataset

   Args:
       seqs:
           DNA muataion character matrix
       ref:
           reference seuence
       rs:
           resampling ratio

   Return:
       np.array:
           LP distance