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Reconstruct tree by OncoNEM#
This example shows how to construct a phylogenetic tree using OncoNEM on a binary single-cell genotype matrix.
import scphylo as scp
# sphinx_gallery_thumbnail_path = "_static/thumbnails/onconem.png"
First, we load a binary test single-cell genotype data.
df_in = scp.datasets.test()
df_in.head()
Next, using scphylo.tl.onconem()
we remove the single-cell noises from the
input.
# TODO: fix
# df_out = scp.tl.onconem(df_in)
# df_out.head()
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)
# is_cf
Total running time of the script: (0 minutes 0.486 seconds)
Estimated memory usage: 9 MB