def test_compute_distances_no_dist(adata_cdr3,
adata_cdr3_mock_distance_calculator,
with_adata2):
adata2 = adata_cdr3 if with_adata2 else None
"""Test for #174. Gracefully handle the case when there are no distances."""
adata_cdr3.obs["IR_VJ_1_junction_aa"] = np.nan
adata_cdr3.obs["IR_VDJ_1_junction_aa"] = np.nan
# test both receptor arms, primary chain only
ir.pp.ir_dist(
adata_cdr3,
adata2,
metric=adata_cdr3_mock_distance_calculator,
sequence="aa",
key_added="ir_dist_aa_custom",
)
cn = ClonotypeNeighbors(
adata_cdr3,
adata2,
receptor_arms="all",
dual_ir="primary_only",
distance_key="ir_dist_aa_custom",
sequence_key="junction_aa",
)
_assert_frame_equal(
cn.clonotypes,
pd.DataFrame({
"IR_VJ_1_junction_aa": ["nan"],
"IR_VDJ_1_junction_aa": ["nan"],
}),
)
dist = cn.compute_distances()
npt.assert_equal(dist.toarray(), np.zeros((1, 1)))
def test_compute_distances(
adata_cdr3,
adata_cdr3_mock_distance_calculator,
comment,
metric,
ctn_kwargs,
expected_clonotype_df,
expected_dist,
n_jobs,
with_adata2,
):
f"""{comment}"""
distance_key = f"ir_dist_aa_{metric}"
metric = adata_cdr3_mock_distance_calculator if metric == "custom" else metric
adata2 = adata_cdr3 if with_adata2 else None
expected_dist = np.array(expected_dist)
ir.pp.ir_dist(adata_cdr3,
adata2,
metric=metric,
sequence="aa",
key_added=distance_key)
cn = ClonotypeNeighbors(
adata_cdr3,
adata2,
distance_key=distance_key,
sequence_key="junction_aa",
n_jobs=n_jobs,
chunksize=1,
**ctn_kwargs,
)
_assert_frame_equal(cn.clonotypes, pd.DataFrame(expected_clonotype_df))
dist = cn.compute_distances()
print(dist)
assert dist.nnz == np.sum(expected_dist != 0)
npt.assert_equal(dist.toarray(), expected_dist)
def test_compute_distances_2(
adata_cdr3_2,
adata_cdr3_mock_distance_calculator,
receptor_arms,
dual_ir,
expected,
n_jobs,
with_adata2,
):
"""Test that `dual_ir` does not impact the second reduction step"""
adata2 = adata_cdr3_2 if with_adata2 else None
ir.pp.ir_dist(
adata_cdr3_2,
adata2,
metric=adata_cdr3_mock_distance_calculator,
sequence="aa",
key_added="ir_dist_aa_custom",
)
cn = ClonotypeNeighbors(
adata_cdr3_2,
adata2,
receptor_arms=receptor_arms,
dual_ir=dual_ir,
distance_key="ir_dist_aa_custom",
sequence_key="junction_aa",
n_jobs=n_jobs,
chunksize=1,
)
dist = cn.compute_distances().toarray()
print(dist)
npt.assert_equal(dist, expected)
def test_compute_distances9(adata_cdr3, adata_cdr3_mock_distance_calculator, n_jobs):
ir.pp.ir_dist(adata_cdr3, metric=adata_cdr3_mock_distance_calculator, sequence="aa")
cn = ClonotypeNeighbors(
adata_cdr3,
receptor_arms="any",
dual_ir="any",
distance_key="ir_dist_aa_custom",
sequence_key="junction_aa",
n_jobs=n_jobs,
chunksize=1,
)
_assert_frame_equal(
cn.clonotypes,
pd.DataFrame(
{
"IR_VJ_1_junction_aa": ["AAA", "AHA", "nan", "AAA", "AAA"],
"IR_VJ_2_junction_aa": ["AHA", "nan", "nan", "AAA", "nan"],
"IR_VDJ_1_junction_aa": ["KKY", "KK", "nan", "LLL", "LLL"],
"IR_VDJ_2_junction_aa": ["KKK", "KKK", "nan", "AAA", "nan"],
}
),
)
dist = cn.compute_distances()
npt.assert_equal(
dist.toarray(),
np.array(
[
[1, 1, 0, 1, 1],
[1, 1, 0, 4, 4],
[0, 0, 0, 0, 0],
[1, 4, 0, 1, 1],
[1, 4, 0, 1, 1],
]
),
)
def test_compute_distances6(adata_cdr3, adata_cdr3_mock_distance_calculator, n_jobs):
# test both receptor arms, primary chain only
ir.pp.ir_dist(adata_cdr3, metric=adata_cdr3_mock_distance_calculator, sequence="aa")
cn = ClonotypeNeighbors(
adata_cdr3,
receptor_arms="all",
dual_ir="primary_only",
distance_key="ir_dist_aa_custom",
sequence_key="junction_aa",
n_jobs=n_jobs,
chunksize=1,
)
_assert_frame_equal(
cn.clonotypes,
pd.DataFrame(
{
"IR_VJ_1_junction_aa": ["AAA", "AHA", "nan", "AAA"],
"IR_VDJ_1_junction_aa": ["KKY", "KK", "nan", "LLL"],
}
),
)
dist = cn.compute_distances().toarray()
print(dist)
npt.assert_equal(
dist,
np.array(
[
[1, 10, 0, 0],
[10, 1, 0, 0],
[0, 0, 0, 0],
[0, 0, 0, 1],
]
),
)
def test_compute_distances5(adata_cdr3, adata_cdr3_mock_distance_calculator, n_jobs):
# test single receptor arm with multiple chains and custom distance
ir.pp.ir_dist(adata_cdr3, metric=adata_cdr3_mock_distance_calculator, sequence="aa")
cn = ClonotypeNeighbors(
adata_cdr3,
receptor_arms="VJ",
dual_ir="all",
distance_key="ir_dist_aa_custom",
sequence_key="junction_aa",
n_jobs=n_jobs,
chunksize=1,
)
_assert_frame_equal(
cn.clonotypes,
pd.DataFrame(
{
"IR_VJ_1_junction_aa": ["AAA", "AHA", "nan", "AAA", "AAA"],
"IR_VJ_2_junction_aa": ["AHA", "nan", "nan", "AAA", "nan"],
}
),
)
dist = cn.compute_distances().toarray()
print(dist)
npt.assert_equal(
dist,
np.array(
[
[1, 0, 0, 4, 0],
[0, 1, 0, 0, 4],
[0, 0, 0, 0, 0],
[4, 0, 0, 1, 0],
[0, 4, 0, 0, 1],
]
),
)
def test_compute_distances3(adata_cdr3, adata_cdr3_mock_distance_calculator, n_jobs):
# test single chain with custom distance
ir.pp.ir_dist(adata_cdr3, metric=adata_cdr3_mock_distance_calculator, sequence="aa")
cn = ClonotypeNeighbors(
adata_cdr3,
receptor_arms="VJ",
dual_ir="primary_only",
distance_key="ir_dist_aa_custom",
sequence_key="junction_aa",
n_jobs=n_jobs,
chunksize=1,
)
_assert_frame_equal(
cn.clonotypes, pd.DataFrame({"IR_VJ_1_junction_aa": ["AAA", "AHA", "nan"]})
)
dist = cn.compute_distances()
assert dist.nnz == 4
dist = dist.toarray()
print(dist)
npt.assert_equal(
dist,
np.array(
[
[1, 4, 0],
[4, 1, 0],
[0, 0, 0],
]
),
)
def test_compute_distances2(adata_cdr3, n_jobs):
# test single receptor arm with multiple chains and identity distance
ir.pp.ir_dist(adata_cdr3, metric="identity", cutoff=0, sequence="aa")
cn = ClonotypeNeighbors(
adata_cdr3,
receptor_arms="VJ",
dual_ir="any",
distance_key="ir_dist_aa_identity",
sequence_key="junction_aa",
n_jobs=n_jobs,
chunksize=1,
)
_assert_frame_equal(
cn.clonotypes,
pd.DataFrame(
{
"IR_VJ_1_junction_aa": ["AAA", "AHA", "nan", "AAA", "AAA"],
"IR_VJ_2_junction_aa": ["AHA", "nan", "nan", "AAA", "nan"],
}
),
)
dist = cn.compute_distances().toarray()
print(dist)
npt.assert_equal(
dist,
np.array(
[
[1, 1, 0, 1, 1],
[1, 1, 0, 0, 0],
[0] * 5,
[1, 0, 0, 1, 1],
[1, 0, 0, 1, 1],
]
),
)
def test_compute_distances1(adata_cdr3, n_jobs):
# test single chain with identity distance
ir.pp.ir_dist(adata_cdr3, metric="identity", cutoff=0, sequence="aa")
cn = ClonotypeNeighbors(
adata_cdr3,
receptor_arms="VJ",
dual_ir="primary_only",
distance_key="ir_dist_aa_identity",
sequence_key="junction_aa",
n_jobs=n_jobs,
chunksize=1,
)
_assert_frame_equal(
cn.clonotypes, pd.DataFrame({"IR_VJ_1_junction_aa": ["AAA", "AHA", "nan"]})
)
dist = cn.compute_distances()
npt.assert_equal(
dist.toarray(),
np.array(
[
[1, 0, 0],
[0, 1, 0],
[0, 0, 0],
]
),
)
def test_compute_distances_second_anndata(
adata_cdr3,
adata_cdr3_2,
comment,
metric,
ctn_kwargs,
expected_clonotype_df,
expected_clonotype_df2,
expected_dist,
swap_query_reference,
):
f"""
Test that the distance calculation works with two different anndata objects
{comment}
"""
query = adata_cdr3 if not swap_query_reference else adata_cdr3_2
reference = adata_cdr3_2 if not swap_query_reference else adata_cdr3
distance_key = f"ir_dist_aa_{metric}"
expected_dist = np.array(expected_dist)
ir.pp.ir_dist(query,
reference,
metric=metric,
sequence="aa",
key_added=distance_key)
cn = ClonotypeNeighbors(
query,
reference,
distance_key=distance_key,
sequence_key="junction_aa",
**ctn_kwargs,
)
_assert_frame_equal(
cn.clonotypes,
pd.DataFrame(expected_clonotype_df
if not swap_query_reference else expected_clonotype_df2),
)
_assert_frame_equal(
cn.clonotypes2,
pd.DataFrame(expected_clonotype_df2
if not swap_query_reference else expected_clonotype_df),
)
dist = cn.compute_distances()
dist = dist.toarray()
print(dist)
npt.assert_equal(
dist, expected_dist if not swap_query_reference else expected_dist.T)
def test_compute_distances13(adata_cdr3, adata_cdr3_mock_distance_calculator):
"""Test for #174. Gracefully handle the case when there are IR. """
adata_cdr3.obs["IR_VJ_1_junction_aa"] = np.nan
adata_cdr3.obs["IR_VDJ_1_junction_aa"] = np.nan
adata_cdr3.obs["has_ir"] = "False"
# test both receptor arms, primary chain only
ir.pp.ir_dist(adata_cdr3, metric=adata_cdr3_mock_distance_calculator, sequence="aa")
with pytest.raises(ValueError):
cn = ClonotypeNeighbors(
adata_cdr3,
receptor_arms="all",
dual_ir="primary_only",
distance_key="ir_dist_aa_custom",
sequence_key="junction_aa",
)
