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())