Show trees of Pango lineages

[hyanwong]

No tests: is there a test ARG we can call a function like this on?

Use like e.g.

pango = "B.1.1.7"
ti.plot_pango_lineage_subtree(pango, collapse_tracked=0.99365, node_labels={}, time_scale="time")

Currently waiting on tskit-dev/tskit#3015 to be merged before this actually works.

[hyanwong]

In the plot title, I would also like to print the name of the file from which the ts was loaded, or some other indicator of the provenance of the ARG. I'm not sure if it's possible to obtain this from the tree sequence or the TreeInfo object?

Here's an example of running ti.plot_pango_lineage_subtree("B.1.1.7", size=(600, 600), collapse_tracked=0.99365, time_scale="time") (root of Alpha) on "clipends-v2-mm_4-noexact-f500-clustloc-mrm_2-rw_10-mgs_10-2021-04-10", having set all the mutation times to UNKNOWN_TIME:

[jeromekelleher]

In the plot title, I would also like to print the name of the file from which the ts was loaded, or some other indicator of the provenance of the ARG. I'm not sure if it's possible to obtain this from the tree sequence or the TreeInfo object?

We can probably make the title an optional argument to this function, which would then easily be parameterised in an analysis notebook.

[jeromekelleher]

No infrastructure yet for systematically testing tree info stuff, I'll do this as soon as we have the data cleaning done.

[hyanwong]

In the plot title, I would also like to print the name of the file from which the ts was loaded, or some other indicator of the provenance of the ARG. I'm not sure if it's possible to obtain this from the tree sequence or the TreeInfo object?

We can probably make the title an optional argument to this function, which would then easily be parameterised in an analysis notebook.

Actually, title is already a parameter, but it's helpful to default to a something that shows some extra detail without having to code it explicitly. I guess I could grab something out of the metadata, or just quote the date the TS was made, the latests sample dates, and the total number of samples.

[jeromekelleher]

the top-level metadata will have the date