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Rename dimensions 'sample_x' and 'sample_y' in PC relate #574

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Merged
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May 18, 2021
Merged

Rename dimensions 'sample_x' and 'sample_y' in PC relate #574

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5 changes: 4 additions & 1 deletion sgkit/stats/pc_relate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,6 +107,7 @@ def pc_relate(

:data:`sgkit.variables.pc_relate_phi_spec`: (S,S) ArrayLike
pairwise recent kinship coefficient matrix as float in [-0.5, 0.5].
The dimensions are named ``samples_0`` and ``samples_1``.

References
----------
Expand Down Expand Up @@ -173,5 +174,7 @@ def pc_relate(
phi = gramian(centered_af) / gramian(stddev)
# NOTE: phi is of shape (S x S), S = num samples
assert phi.shape == (call_g.shape[1],) * 2
new_ds = create_dataset({variables.pc_relate_phi: (("sample_x", "sample_y"), phi)})
new_ds = create_dataset(
{variables.pc_relate_phi: (("samples_0", "samples_1"), phi)}
)
return conditional_merge_datasets(ds, new_ds, merge)
4 changes: 2 additions & 2 deletions sgkit/tests/test_pc_relate.py
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Expand Up @@ -122,7 +122,7 @@ def test_pc_relate__identical_sample_should_be_05() -> None:
g.call_genotype.loc[dict(samples=8)] = g.call_genotype.isel(samples=0)
phi = pc_relate(g)
assert phi.pc_relate_phi.shape == (n_samples, n_samples)
assert np.allclose(phi.pc_relate_phi.isel(sample_x=8, sample_y=0), 0.5, atol=0.1)
assert np.allclose(phi.pc_relate_phi.isel(samples_0=8, samples_1=0), 0.5, atol=0.1)


def test_pc_relate__parent_child_relationship() -> None:
Expand Down Expand Up @@ -164,7 +164,7 @@ def simulate_new_generation(ds: xr.Dataset) -> xr.Dataset:
ds["pc_relate_phi"]
.to_series()
.reset_index()
.pipe(lambda df: df.loc[df.sample_x >= df.sample_y]["pc_relate_phi"])
.pipe(lambda df: df.loc[df.samples_0 >= df.samples_1]["pc_relate_phi"])
.pipe(
pd.cut,
bins=[p for phi in [0, 0.25, 0.5] for p in [phi - 0.1, phi + 0.1]],
Expand Down