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Fixed set_fdr for tascCODA models #411

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merged 3 commits into from
Oct 24, 2023
Merged

Fixed set_fdr for tascCODA models #411

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01f63c5
Fixed set_fdr for tascCODA models
Lilly-May Oct 24, 2023
517d1be
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 24, 2023
1341604
Update pertpy/tools/_coda/_base_coda.py
Lilly-May Oct 24, 2023
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6 changes: 1 addition & 5 deletions docs/installation.md
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Expand Up @@ -77,11 +77,7 @@ Follow these steps to install pertpy on an Apple Silicon machine (tested on a Ma
$ pip install .
```

Now you're ready to use pertpy as usual within the environment (`import pertpy`).

```

```
Now you're ready to use pertpy as usual within the environment (`import pertpy`).

[github repo]: https://github.com/theislab/pertpy
[pip]: https://pip.pypa.io
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10 changes: 9 additions & 1 deletion pertpy/tools/_coda/_base_coda.py
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Expand Up @@ -1046,7 +1046,15 @@ def set_fdr(self, data: AnnData | MuData, est_fdr: float, modality_key: str = "c
if isinstance(data, AnnData):
sample_adata = data

intercept_df, effect_df = self.summary_prepare(sample_adata, est_fdr, *args, **kwargs) # type: ignore
if sample_adata.uns["scCODA_params"]["model_type"] == "classic":
intercept_df, effect_df = self.summary_prepare(sample_adata, est_fdr, *args, **kwargs) # type: ignore
elif sample_adata.uns["scCODA_params"]["model_type"] == "tree_agg":
intercept_df, effect_df, node_df = self.summary_prepare(sample_adata, est_fdr, *args, **kwargs) # type: ignore
# Save node df in `sample_adata.uns`
sample_adata.uns["scCODA_params"]["node_df"] = node_df
else:
raise ValueError("No valid model type!")

sample_adata.varm["intercept_df"] = intercept_df
for cov in effect_df.index.get_level_values("Covariate"):
sample_adata.varm[f"effect_df_{cov}"] = effect_df.loc[cov, :]
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1 change: 0 additions & 1 deletion pertpy/tools/_coda/_tasccoda.py
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Expand Up @@ -664,7 +664,6 @@ def set_fdr(self, data: AnnData | MuData, est_fdr: float, modality_key: str = "c
>>> )
>>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
>>> tasccoda.set_fdr(mdata, est_fdr=0.4)
#TODO: Not working (throws error, because too many values to unpack -> Correct set_fdr first)
"""
return super().set_fdr(data, est_fdr, modality_key, *args, **kwargs)

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