def test_trim_dense(self): gene_data = TestDataSingleCellLike.gene_metadata gene_data.index = gene_data.iloc[:, 0] adata = InferelatorData(self.expr, gene_data=gene_data) adata.trim_genes(remove_constant_genes=False) pdt.assert_frame_equal( self.expr.reindex(CORRECT_GENES_INTERSECT, axis=1).astype(np.int32), adata._adata.to_df()) adata.trim_genes(remove_constant_genes=True) pdt.assert_frame_equal( self.expr.reindex(CORRECT_GENES_NZ_VAR, axis=1).astype(np.int32), adata._adata.to_df())
def test_trim_sparse(self): gene_data = TestDataSingleCellLike.gene_metadata gene_data.index = gene_data.iloc[:, 0] adata_sparse = InferelatorData( sparse.csr_matrix( TestDataSingleCellLike.expression_matrix.values.T), gene_names=TestDataSingleCellLike.expression_matrix.index, meta_data=TestDataSingleCellLike.meta_data.copy(), gene_data=gene_data) adata_sparse.trim_genes(remove_constant_genes=False) pdt.assert_frame_equal( self.expr.reindex(CORRECT_GENES_INTERSECT, axis=1), adata_sparse._adata.to_df()) adata_sparse.trim_genes(remove_constant_genes=True) pdt.assert_frame_equal(self.expr.reindex(CORRECT_GENES_NZ_VAR, axis=1), adata_sparse._adata.to_df())