hapsburg.figures.plot_posterior
===============================

.. py:module:: hapsburg.figures.plot_posterior

.. autoapi-nested-parse::

   Main Inference Class for HMM. Wrapper for Inerence of Posterior.
   @ Author: Harald Ringbauer, 2019, All rights reserved



Functions
---------

.. autoapisummary::

   hapsburg.figures.plot_posterior.load_data
   hapsburg.figures.plot_posterior.process_read_counts
   hapsburg.figures.plot_posterior.plot_posterior_cm
   hapsburg.figures.plot_posterior.plot_viterbi
   hapsburg.figures.plot_posterior.plot_posterior


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

.. py:function:: load_data(folder='../Simulated/Example0/', empirical=False, fullpost=False, viterbi=False, readcounts=True)

   Load and return the Data from one Data Folder


.. py:function:: process_read_counts(read_counts, m=1)

   Return Readcount that have at least m reads for both Ref and Alt


.. py:function:: plot_posterior_cm(folder='../Simulated/Test20r/', savepath='', empirical=True, plot=True, cm_lim=[], ylim=[-0.1, 1.25], m=1, groundtruth=False, readcount=False, plot_hets=True, plot_calls=True, plot_post=True, scale=1.0, min_cm=1.0, yticks=[0.0, 0.2, 0.4, 0.6, 0.8, 1.0], xlabel='Map position [centimorgan]', figsize=(14, 4), title='', post_c='maroon', het_c='blue')

   Plot Viterbi Path of Haplotype copying.
   save: Whether to save the results.
   empirical: If true, do not load and plot latent states
   cm_lim: What Area to Zoom In (CentiMorgan)
   m: How many reads for ref and alt
   yticks: Where to place the Y ticks
   groundtruth: Whether to plot Ground Truth (saved as csv).
   Only used in simulated data with known ROH
   plot_hets: Whether to plot Heterozygote Markers
   plot_calls: Whether to plot Calls
   plot_post: Whether to plot posterior
   plot: Whether to show the plot in python


.. py:function:: plot_viterbi(folder='../Simulated/Test20r/', save=True, empirical=False)

   Plot Viterbi Path of Haplotype copying


.. py:function:: plot_posterior(folder='../Simulated/Test20r/', save=True, empirical=False)

   Plot Viterbi Path of Haplotype copying.
   save: Whether to save the results.
   empirical: If true, do not load and plot latent states