scPhyloX.tools.utils
====================

.. py:module:: scPhyloX.tools.utils


Functions
---------

.. autoapisummary::

   scPhyloX.tools.utils.corr_plot
   scPhyloX.tools.utils.colless_index
   scPhyloX.tools.utils.colless_index_corrected
   scPhyloX.tools.utils.ext_gen
   scPhyloX.tools.utils.ext_cid
   scPhyloX.tools.utils.reconstruct


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

.. py:function:: corr_plot(x, y, ax, stats='pearson', r0_x=None, r0_y=None, r1_x=None, r1_y=None, line='fit', alternative='two-sided', fontsize=10)

   Draw a scatter plot of the two sets of data and show their correlation coefficients

   Args:
       x: 
           data1
       y: 
           data2
       ax: 
           axes to draw scatter on
       stats: 
           pearson or spearman
       r0_x, r0_y, r1_x, r1_y: 
           locations to label the correlation coefficient and the p-value
       line:
           fit or diag, fit for linear regression
       alternative:
           greater, less or two-sided
       fontsize:
           fontsize
   Return:
       matplotlib.axes


.. py:function:: colless_index(tree)

   calculate Colless' index

   Args:
       tree:
           Phylogenetic tree
   Return:
       float:
           Colless' index


.. py:function:: colless_index_corrected(tree)

   calculate corrected Colless' index

   Args:
       tree:
           Phylogenetic tree
   Return:
       float:
           corrected Colless' index


.. py:function:: ext_gen(cell)

   Extract generation with given cell name


.. py:function:: ext_cid(cell)

   Extract cell id with given cell name


.. py:function:: reconstruct(lineage_info, sel_cells, file_name=None)

   Reconstruct phylogenetic tree of simulation data

   Args:
       lineage_info:
           system.lineage_info
       sel_cells:
           cells to build phylogenetic tree
       file_name:
           path to save tree. if None, just return
   Return:
       text newick tree