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doubletdetection/doubletdetection.py

Lines changed: 7 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -318,8 +318,13 @@ def _one_fit(self):
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if self.verbose:
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print("Running PCA...")
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# "auto" solver faster for dense matrices
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solver="arpack" if sp_sparse.issparse(aug_counts.X) else "auto"
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sc.tl.pca(aug_counts, n_comps=self.n_components, random_state=self.random_state, svd_solver=solver)
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solver = "arpack" if sp_sparse.issparse(aug_counts.X) else "auto"
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sc.tl.pca(
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aug_counts,
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n_comps=self.n_components,
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random_state=self.random_state,
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svd_solver=solver,
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)
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if self.verbose:
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print("Clustering augmented data set...\n")
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if self.clustering_algorithm == "phenograph":

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