Load a specific branch

[IgnatG]

Does anyone know if it's possible to load only a part of the tree?

See below an example where I have the full tree loaded by default. I was wondering if there is a way to load only the tree on the right-hand-side (which is a specific part of the original one)

[stephenshank]

Dear @IgnatG,

As far as I know, this functionality does not exist in phylotree.js at present. There seems to be a function to do this in ETE3: http://etetoolkit.org/docs/latest/reference/reference_tree.html#ete3.TreeNode.prune

Let's keep this issue open since this would definitely be useful to have and others may want to chime in. Thanks for pointing out an interesting feature!

Best, Stephen

[spond]

Dear @IgnatG,

When you say

to load only the tree on the right-hand-side

do you mean

1. Load the entire tree, display only a substree
2. Load only the subtree, ie. ignore the rest of the tree when the Newick string is parsed

Best, Sergei

[stephenshank]

Dear @IgnatG,

Also it definitely could be done. Perhaps by programmatically hiding, see the following functionality which is part of the default user interface. I just meant that there is no equivalent function to ETE3's to do this immediately at the moment.

Best, Stephen

[IgnatG]

Dear @spond,

Ideally, it would be option 2 to avoid having to load the entire tree. But option 1 is fine as well. I don't have a personal preference as long as it achieves the goal.

My scenario is as follows: I have a newick tree saved in a variable (or file). It's a big tree so I don't want to look at the whole thing at once, but rather only on specific parts/branches at a time. This example helps as it has 2 coloured clusters:

In this case, I'd want to look first at Cluster 1 only - so only this one would be visible at a time. But I should be able to look at Cluster 2 as well if I need to (but again, only this one would be visible). Or, I should be able to go back to see the entire tree if needed.

Let me know if this helps.

Best wishes, Gabriel

[IgnatG]

Dear @stephenshank ,

Yes, this is what I'm doing now. I'm actually doing it in the code as well through tree.delete_a_node(node) and it hides the branch as expected.

I was just curious to see if there is a better way of doing it as sometimes I could have multiple branches that need hiding. Of course, this can be achieved through a loop, but that's a back-up plan

Thank you for your help though!

Best wishes, Gabriel