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Exclusion of observed variables from posterior #144

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Exclusion of observed variables from posterior #144

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356f3ca
exclusion of observed variables from posterior
vitkl Apr 16, 2022
e36c58c
black
vitkl Apr 16, 2022
11b6b50
Fix scvi-tools to version <0.16.0
vitkl Apr 16, 2022
e80cfe8
fix scvi-tools>=0.15.3<0.15.5
vitkl Apr 16, 2022
0c763da
fix jax version instead of scvi-tools
vitkl Apr 16, 2022
fb6715f
fix jaxlib version
vitkl Apr 16, 2022
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2 changes: 2 additions & 0 deletions setup.cfg
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Expand Up @@ -18,6 +18,8 @@ install_requires =
scvi-tools>=0.15.3
torch>=1.9.0
pymc3>=3.8<3.10
jax>=0.3,<=0.3.6
jaxlib>=0.1.65,<=0.3.5
arviz==0.10.0
numpy
pandas
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4 changes: 4 additions & 0 deletions tests/test_cell2location.py
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Expand Up @@ -24,6 +24,8 @@ def test_cell2location():
sc_model.train(max_epochs=1, batch_size=1000)
# export the estimated cell abundance (summary of the posterior distribution)
dataset = sc_model.export_posterior(dataset, sample_kwargs={"num_samples": 10})
# test exclusion of observed variables from posterior sampling
assert "data_target" not in dataset.uns["mod"]["post_sample_means"].keys()
# test plot_QC
sc_model.plot_QC()
# test save/load
Expand All @@ -47,6 +49,8 @@ def test_cell2location():
# export the estimated cell abundance (summary of the posterior distribution)
# full data
dataset = st_model.export_posterior(dataset, sample_kwargs={"num_samples": 10, "batch_size": st_model.adata.n_obs})
# test exclusion of observed variables from posterior sampling
assert "data_target" not in dataset.uns["mod"]["post_sample_means"].keys()
## minibatches of locations ##
Cell2location.setup_anndata(dataset, batch_key="batch")
st_model = Cell2location(dataset, cell_state_df=inf_aver, N_cells_per_location=30, detection_alpha=200)
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