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,
sequence_length=sequence_length,
recombination_rate=rho/4/sequence_length)
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)
divplot
