Drawing a tree with subset of sample nodes and/or larger dots for sample nodes

[janaobsteter]

I am trying to draw a nice tree and I'm failing.
This is my plot for a specific location in the honeybee genome. I have some samples with known subspecies (colours) and the majority of them are hybrids, which I've coloured in white. Is there any way to:

1. Draw a tree for a subset of the samples (just the coloured ones)
2. To increase the size of the sample nodes

The code I'm using at the moment is very simple:

ts10 = tskit.load("Chr10.trees")
yellowtree = ts10.at(11506337)
yellowtree.draw(
    path="yellowtreeStart.svg",
    height=700,
    width=1200,
    node_labels={},
    node_colours=colours_for_node,
)

Any help is much appreciated!

[hyanwong]

For plotting a subset of the samples, you can use simplify(): there's an example in https://tskit.dev/tutorials/getting_started.html#processing-trees but you are quite right that it is a bit hidden, and we should also give an example in the "viz" tutorial (I've opened an issue: tskit-dev/tutorials#182).

To increase the size of the nodes, you can use draw_svg(symbol_size=5) (pick whatever number seems right for your viz). If you only want to increase the size of the sample nodes, you could, for example, hide the other nodes by adding ".node:not(.leaf) > .sym {display: none}" to the style (see https://tskit.dev/tutorials/viz.html#restricting-styling).

Note, however, that if you use the more sophisticated draw_svg() method you will need to colour the populations using css. There's an example in the tutorial and some discussion at #2330 (comment)

[hyanwong]

Also note a little hack at #2365 which might make it easier to see clusters:

[janaobsteter]

Thanks! I think I'll manage now :)

[hyanwong]

Maybe whatever SVG program you are using doesn't like the ":not" selector. You could resort to the chromium hack: https://tskit.dev/tutorials/viz.html#sec-tskit-viz-converting-note

[janaobsteter]

Argh, I was opening it in Inkscape. Never would have of that being a problem, thanks!

[hyanwong]

Yeah, Inkscape support for some of the CSS is annoyingly patchy.

[jeromekelleher]

Maybe worth a "warning" admonition in the docs @hyanwong?

[hyanwong]

It looks like Inkscape doesn't support the "visibility" property. I could just change that to "display: none" in the example instead.