(fix): obs filtering #148
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(fix): obs filtering #148
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ilan-gold
commented
Oct 16, 2024
muon/_core/preproc.py
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| # Collect elements to subset | ||
| # NOTE: accessing them after subsetting .obs | ||
| # will fail due to _validate_value() | ||
| obsm = dict(data.obsm) |
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probably need to use _remove_unused_categories on the dataframe - please open an issue in anndata about making this public
ilan-gold
commented
Oct 16, 2024
tests/test_muon_preproc.py
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| A = pbmc3k_processed[:500,].copy() | ||
| B = pbmc3k_processed[500:,].copy() | ||
| mdata = mu.MuData({"A": A, "B": B}) | ||
| np.random.seed(42) | ||
| var_sel = np.random.choice(np.array([0, 1]), size=mdata.n_vars, replace=True) | ||
| mdata.var["sel"] = var_sel | ||
| mu.pp.filter_var(mdata, "sel", lambda y: y == 1) | ||
| assert mdata.shape[1] == int(np.sum(var_sel)) |
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Update this test as well to check the full object like assert_equal(mdata["B"], B_subset)
ilan-gold
commented
Oct 16, 2024
muon/_core/preproc.py
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| @@ -756,6 +764,18 @@ def func(x): | |||
| data.raw._n_obs = data.raw.X.shape[0] | |||
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| else: | |||
| # Subset .obs | |||
| data._obs = data.obs[obs_subset] | |||
| data._n_obs = data.obs.shape[0] | |||
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Not sure this is necessary for AnnData. Also please consider de-dupping all this logic - you can use getattr(data, f"{key}m") and make key: Literal["obs", "var"] an argument to a helper
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Fixes #146