New tskit_arg_visualizer allows recombinants to be shown effectively

[hyanwong]

@kitchensjn has made a change to the latest dev version of tskit_arg_visualizer which means that it is now a very effective tool for examining small groups of Pango samples, such as most of the Pango-X lineages. Namely, you can pass a set of nodes (e.g. from from ti.pango_lineage_samples) into the d3arg.draw_nodes() function, along with a parameter degree=(parent_levels, child_levels) value, and the ancestry of those samples is shown. E.g.:

import sc2ts
import tskit_arg_visualizer as argviz

filename = "v1-beta1_2022-07-25.il.dated.tsz"
ts = tszip.load(filename)
ti = sc2ts.TreeInfo(ts)
d3arg = argviz.D3ARG.from_ts(ts, progress=True)
d3arg.draw_nodes(
    ti.pango_lineage_samples["XA"],
    degree=(20, 1),   # show up to 2 parent levels, but not descendant children
    show_mutations=True,
    y_axis_scale="time",
    include_mutation_labels=False,
    condense_mutations=False,
)

NB, this may require the following in a different cell:

%%javascript
// necessary incantation to get the tskit_arg_visualizer to display on some systems
var script = document.createElement('script');
script.type = 'text/javascript';
script.src = 'https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js';
document.head.appendChild(script);

Here's an example, with XA coloured in magenta. In this case it would have been the same as specifying the recombination node, but in cases where pango lineages have been assigned to different recombinants, this approach should immediately identify what is going on.