Comparing two trees by TPTED

This example shows how to compare/measure two inferred genotype data (trees).

import scphylo as scp

# sphinx_gallery_thumbnail_path = "_static/thumbnails/tpted.png"

First, we load two binary test single-cell genotype data.

grnd = scp.io.read(
    scp.ul.get_file("scphylo.datasets/test/fp_0-fn_0-na_0.ground.CFMatrix")
)
sol = scp.io.read(
    scp.ul.get_file("scphylo.datasets/test/fp_1-fn_0.1-na_0.bnb.CFMatrix")
)

Calculating the tumor phylogeny tree edit distance measure (TPTED).

scp.tl.tpted(grnd, sol)

0.8811881188118812

Estimated memory usage: 9 MB