Add interactive applet on diversity along a recombining region (#12)

book/_toc.yml

@@ -12,6 +12,7 @@ parts:
     - file: markdown/kingman_coalsecent/model_for_data
     - file: markdown/kingman_coalsecent/trees
     - file: markdown/kingman_coalsecent/trees_with_recombination
+    - file: markdown/kingman_coalsecent/recombination_diversity
     - file: markdown/kingman_coalsecent/mutation_frequencies
     - file: markdown/kingman_coalsecent/expectations
     - file: markdown/kingman_coalsecent/distributions

book/markdown/kingman_coalsecent/recombination_diversity.md

@@ -0,0 +1,37 @@
+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
+
+# Variation in diversity along a recombining genome
+
+```{code-cell} python
+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
+```