def test_dense_subsample_genes(self):
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
n_genes = dataset.nb_genes
n_top = n_genes // 2
dataset.subsample_genes(new_n_genes=n_top, mode="cell_ranger")
assert dataset.nb_genes == n_top
# With Seurat v2
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
dataset.subsample_genes(new_n_genes=n_top, mode="seurat_v2")
assert dataset.nb_genes == n_top
# With Seurat v3
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
dataset.subsample_genes(new_n_genes=n_top, mode="seurat_v3")
assert dataset.nb_genes == n_top
# With Poisson zeros
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
dataset.subsample_genes(new_n_genes=n_top, mode="poisson_zeros")
assert dataset.nb_genes == n_top
# make sure constant genes have low scores
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
dataset.X[:, -1] = np.zeros_like(dataset.X[:, -1])
df = dataset._highly_variable_genes(n_top_genes=n_top,
flavor="seurat_v3")
assert df.loc[str(dataset.nb_genes -
1)]["highly_variable_median_variance"] == 0
def test_batch_correction(self):
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
n_genes = dataset.nb_genes
n_top = n_genes // 2
dataset._highly_variable_genes(n_bins=3, flavor="seurat_v2")
df = dataset._highly_variable_genes(n_bins=3,
n_top_genes=n_top,
flavor="seurat_v2")
assert df["highly_variable"].sum() >= n_top
dataset.filter_genes_by_count(2, per_batch=True)
dataset.subsample_genes(new_n_genes=n_top)
new_genes = dataset.nb_genes
assert n_genes > new_genes, "subsample_genes did not filter out genes"
def test_batch_correction(self):
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
n_genes = dataset.nb_genes
n_top = n_genes // 2
dataset._highly_variable_genes(n_bins=3, flavor="seurat_v2")
df = dataset._highly_variable_genes(n_bins=3,
n_top_genes=n_top,
flavor="seurat_v2")
assert df["highly_variable"].sum() >= n_top
dataset.filter_genes_by_count(2, per_batch=True)
dataset.subsample_genes(new_n_genes=n_top)
new_genes = dataset.nb_genes
assert n_genes > new_genes, "subsample_genes did not filter out genes"
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
n_genes = dataset.nb_genes
n_top = n_genes // 2
df = dataset._highly_variable_genes(n_bins=3,
flavor="seurat_v2",
batch_correction=False,
n_top_genes=n_top)
assert ("highly_variable_nbatches" not in df.columns
), "HVG dataframe should not contain batch information"
df = dataset._highly_variable_genes(n_bins=3,
flavor="seurat_v2",
batch_correction=True)
assert "highly_variable_nbatches" in df.columns
assert "highly_variable_intersection" in df.columns
df = dataset._highly_variable_genes(n_bins=3,
flavor="seurat_v3",
batch_correction=False,
n_top_genes=n_top)
assert ("highly_variable_nbatches" not in df.columns
), "HVG dataframe should not contain batch information"
df = dataset._highly_variable_genes(n_bins=3,
flavor="seurat_v3",
batch_correction=True,
n_top_genes=n_top)
assert "highly_variable_nbatches" in df.columns
assert "highly_variable_intersection" in df.columns
def test_dense_subsample_genes(self):
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
n_genes = dataset.nb_genes
n_top = n_genes // 2
dataset.subsample_genes(new_n_genes=n_top, mode="cell_ranger")
assert dataset.nb_genes == n_top
# With Seurat v2
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
dataset.subsample_genes(new_n_genes=n_top, mode="seurat_v2")
assert dataset.nb_genes == n_top
# With Seurat v3
dataset = SyntheticDataset(batch_size=100, nb_genes=100, n_batches=3)
dataset.subsample_genes(new_n_genes=n_top, mode="seurat_v3")
assert dataset.nb_genes == n_top
