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Reconstruct tree by SCITE#
This example shows how to construct a phylogenetic tree using SCITE on a binary single-cell genotype matrix.
import scphylo as scp
# sphinx_gallery_thumbnail_path = "_static/thumbnails/scite.png"
First, we load a binary test single-cell genotype data.
df_in = scp.datasets.test()
df_in.head()
Next, using scphylo.tl.scite()
we remove the single-cell noises from the
input.
df_out = scp.tl.scite(df_in, alpha=0.0000001, beta=0.1, n_restarts=3, n_iters=1000)
df_out.head()
running SCITE with alpha=1e-07, beta=0.1, n_iters=1000, n_restarts=3
input -- size: 20x20
input -- 0: 226#, 56.5%
input -- 1: 94#, 23.5%
input -- NA: 80#, 20.0%
input -- CF: False
output -- size: 20x20
output -- 0: 243#, 60.8%
output -- 1: 157#, 39.2%
output -- NA: 0#, 0.0%
output -- CF: True
output -- time: 0.0s (0:00:00.024121)
flips -- #0->1: 37
flips -- #1->0: 0
flips -- #NA->0: 54
flips -- #NA->1: 26
rates -- FN: 0.282
rates -- FP: 0.00000000
rates -- NA: 0.200
score -- NLL: 95.09955581261663
score: -78.03716700617949
beta: 0.2961948014929035
Finally, using scphylo.ul.is_conflict_free_gusfield()
we check whether the
inferred genotype matrix is conflict-free or not.
is_cf = scp.ul.is_conflict_free_gusfield(df_out)
print(is_cf)
True
Total running time of the script: (0 minutes 0.871 seconds)
Estimated memory usage: 14 MB