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Reconstruct tree by Trisicell-PartF#
This example shows how to assess a phylogenetic tree using Trisicell-PartF on a binary single-cell genotype matrix.
import scphylo as scp
# sphinx_gallery_thumbnail_path = "_static/thumbnails/trisicell-partf.png"
First, we load a binary test single-cell genotype data.
df_in = scp.datasets.test()
df_in.head()
Then, using scphylo.tl.partf()
we calculate the probability of cell6 and
cell17 seeded by mut12
probs = scp.tl.partition_function(
df_in,
alpha=0.000001,
beta=0.1,
n_samples=100,
n_batches=10,
muts=["mut12"],
cells=["cell6", "cell17"],
)
probs.mean(axis=1).round(4).values[0]
elapsed time: 0:00:04.770798
0.8948
Total running time of the script: (0 minutes 5.207 seconds)
Estimated memory usage: 10 MB