Reconstruct tree by gpps

This example shows how to construct a phylogenetic tree using gpps on a binary single-cell genotype matrix.

import scphylo as scp

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

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

df_in = scp.datasets.test()
df_in.head()

	mut0	mut1	mut2	mut3	mut4	mut5	mut6	mut7	mut8	mut9	mut10	mut11	mut12	mut13	mut14	mut15	mut16	mut17	mut18	mut19
cellIDxmutID
cell0	1	1	1	1	1	1	1	0	3	3	0	3	0	0	0	3	0	0	0	0
cell1	3	0	0	0	0	0	3	0	1	1	3	1	0	0	3	0	0	1	1	1
cell2	0	0	0	0	0	0	0	1	1	3	1	1	0	0	3	1	1	1	1	0
cell3	0	0	0	0	0	0	0	3	1	0	0	1	0	0	0	1	1	1	0	0
cell4	0	0	0	0	0	0	0	1	1	1	1	1	0	0	3	0	0	0	0	0

Next, using scphylo.tl.gpps() we remove the single-cell noises from the input.

# TODO: fix
# df_out = scp.tl.gpps(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

Estimated memory usage: 9 MB