Get trunk and branch clusters

[itigupta2429]

Hi Team, I wanted to get the trunk and branch wise cluster information from the .npz file. For Example:

In this case: Trunk = clusters 0 to 8 branch1 = cluster 9 branch2 = cluster 10 The tree structure in .npz file looks like: tree_0 Out[2]: array([0, 1, 2, 3, 4, 5, 6, 7, 8, 8]) Could you please help me with the same?

[ethanumn]

It seems like you're looking for something like the answer in #35

Alternatively, Orchard (https://github.com/morrislab/orchard/) has some built-in functionality to do this type of analysis. There's a function that will split apart a tree into all of its branching events.

You could either install this package or just copy and paste the function that does this located in /orchard/lib/cluster/utils.py

import os, sys
import numpy as np

sys.path.append("/path/to/orchard", "lib", "cluster"))
from utils import dfs_find_lineages

parents = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 8])
branches, _ = dfs_find_lineages(parents)

print("Trunk", branches[0])
for i in range(1, len(branches)):
    print(f"Branch {i} = ", branches[i])

This will output the following:

Trunk [1, 2, 3, 4, 5, 6, 7, 8]
Branch 1 =  [10]
Branch 2 =  [9]

[itigupta2429]

@ethanumn Thanks a lot for your quick response. It Worked!