hapsburg.figures.plot_individual_roh
====================================

.. py:module:: hapsburg.figures.plot_individual_roh

.. autoapi-nested-parse::

   Plotting function to plot karyotype plot of ROH from hapsburg output
   @ Author: Harald Ringbauer, 2019, All rights reserved



Functions
---------

.. autoapisummary::

   hapsburg.figures.plot_individual_roh.load_roh
   hapsburg.figures.plot_individual_roh.post_process_roh_df1
   hapsburg.figures.plot_individual_roh.chrom_length
   hapsburg.figures.plot_individual_roh.load_individual_roh
   hapsburg.figures.plot_individual_roh.load_bad_areas
   hapsburg.figures.plot_individual_roh.plot_chromosome
   hapsburg.figures.plot_individual_roh.plot_roh_individual
   hapsburg.figures.plot_individual_roh.expected_block_pdf
   hapsburg.figures.plot_individual_roh.expected_block_pdf_chromosomes
   hapsburg.figures.plot_individual_roh.coal_prob
   hapsburg.figures.plot_individual_roh.exp_blocks_full_individual
   hapsburg.figures.plot_individual_roh.plot_pde_individual


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

.. py:function:: load_roh(iid, ch, path_folder='./Empirical/1240k/', prefix_out='e01/')

   Load the ROH Dataframe for Individual iid and
   Chromosome ch


.. py:function:: post_process_roh_df1(df, min_cm=4, snp_cm=100, output=False)

   Post Process ROH Dataframe.
   min_cm: Minimum Length in CentiMorgan
   snp_cm: How many SNPs per CentiMorgan


.. py:function:: chrom_length(ch, ch_lengths=[], output=False)

   Get and return length of Chromosome ch
   If ch_lengths not given, use default (from Eigenstrat map).
   Atm only do autosomes!


.. py:function:: load_individual_roh(iid, min_cm=4, gap=0.0, snp_cm=50, path_folder='./Empirical/1240k/', prefix_out='', folder='./Empirical/1240k/', output=False)

   Load ROH of one Individual


.. py:function:: load_bad_areas(path='./Data/1000Genomes/Markers/1240k/snp_density.csv', min_snps=50)

   Load areas of low SNP density, and return list of Dataframes
   (one for each chromosome)


.. py:function:: plot_chromosome(ax, l, x_pos, lw=24, df_roh=[], df_low=[])

   Plot a Chromosome of length l with centromer ctr on ax
   at x_pos


.. py:function:: plot_roh_individual(iid='MA89', fs=12, figsize=(8, 8), savepath='', min_cm=4, snp_cm=50, gap=0.0, folder='./Empirical/1240k/MarcusAncs/', prefix_out='', plot_bad=True, title='True', output=False)

   Plot ROH in one ancient Individual.
   gap: What Gap to Merge [in cM!]
   prefix_out: If there is a folder before indivual data, e.g. e01/


.. py:function:: expected_block_pdf(x, chr_l, m)

   Gives back the pdfs for Blocks of Length l [Morgan]
   on a Chromosome of Length [Morgan].
   m: Nr of Meiosis.
   Return PDF (per Morgan)


.. py:function:: expected_block_pdf_chromosomes(x, chr_lgts, m)

   Calculate the PDF of ROH blocks of length x [Morgan]
   for m Recombination events
   x: Can be Array
   chr_lgts: Array of all chromosome lengths [in Morgan]
   Return PDF (per Morgan)


.. py:function:: coal_prob(m, comm_anc=1)

   Calculate Coalescence Probability.
   m: Nr of Meiosis
   comm_anc: How many common ancestors


.. py:function:: exp_blocks_full_individual(x, m, comm_anc=1)

   Calculates the Expected Nr of ROH Blocks per Morgan for full Individual
   x: Array of Block Lenths
   m: Nr of Meisois
   comm_anc: Nr of Ancestry Loops


.. py:function:: plot_pde_individual(iid='MA89', figsize=(8, 6), min_cm=4, snp_cm=50, bw_cm=4, kde_plot=False, plotlim=[4, 100], savepath='', folder='./Empirical/1240k/', prefix_out='e01/', output=False, gap=0.0, lw_curve=3, comm_ancs=[4, 4, 4, 2], ms=[6, 5, 4, 3], labels=['First Cousins', 'Aunt/Nephew', 'Full Siblings', 'Parent/Offpsring'], cs=['red', 'green', 'orange', 'gray'], title='', leg_loc='upper right')

   Plot Histograms/PDEs of ROH Distribution for one Individual (iid)
   If list of k iids given, load all ROH and plot all of them, and the expected value for k individuals.
   bw_cm: Length of one Bin (in cM)
   comm_ancs: How many common ancestors to plot [list] In number of haplotypes
   ms: How many meiosis to plot [list]
   labels: what labels do they have [list]
   cs: what colors to plot [list]
   kde_plot: If True fit and plot a KDE to the ROH histogram