Variation in diversity along a recombining genome (interactive Python)

This notebook is interactive. See here for more information.

This applet is another take on the concepts shown in Figure 5 of Hudson [1990].

import msprime
import numpy as np
import panel as pn
import holoviews as hv

hv.extension('bokeh', 'matplotlib')

def branch_diversity_along_tree(rho, n, sequence_length=1e6, num_windows=500):
    wins = np.linspace(0, sequence_length, num_windows)
    mids = (wins[1:] - wins[:1])/2
    ts = msprime.sim_ancestry(n, ploidy=1,
    assert ts.num_samples == n
    diversity = ts.diversity(windows=wins, mode="branch").flatten()
    return hv.Curve((mids, diversity)).opts(tools=["box_select"]).redim(y=hv.Dimension('y',
                                                                                       range=(0, 1.1*diversity.max()))).opts(xlabel="Window midpoint", ylabel="Diversity (branch stat)")

divplot = hv.DynamicMap(branch_diversity_along_tree,
                        kdims=['rho', 'n']).redim.range(rho=(0, 1000), n=(10, 100)).opts(framewise=True, width=500)