scverse / pertpy

Perturbation Analysis in the scverse ecosystem.
https://pertpy.readthedocs.io/en/latest/
MIT License
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ete3 throws an error when calling draw_effects() #520

Closed namsaraeva closed 4 months ago

namsaraeva commented 5 months ago

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An ImportError occured when running example code for Tasccoda:

import pertpy as pt

adata = pt.dt.tasccoda_example()
tasccoda = [pt.tl](http://pt.tl/).Tasccoda()
mdata = tasccoda.load(
adata, type=“sample_level”,
levels_agg=[“Major_l1", “Major_l2”, “Major_l3", “Major_l4”, “Cluster”], key_added=“lineage”, add_level_name=True)
mdata = tasccoda.prepare(mdata, formula=“Health”, reference_cell_type=“automatic”, tree_key=“lineage”, pen_args={“phi”: 0})
tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
pt.pl.coda.draw_effects(mdata, covariate=“Health[T.Inflamed]“, tree=“lineage”)

pt.pl.coda.draw_effects() throws Import Error: to use tasscoda please install ete3 with pip install ete3 even though ete3 is installed and can be verified with import ete3 running without any issues.

grafik

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namsaraeva commented 5 months ago

session_info.txt