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Change the default number of nearest neighbors search in Ingest #1111

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Merged
merged 3 commits into from
May 18, 2020
Merged

Change the default number of nearest neighbors search in Ingest #1111

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e24202c
use n_neighbors from sc.tl.neighbors
Koncopd Mar 17, 2020
1304319
add test
Koncopd May 17, 2020
354fc87
fix pynndescent conflict
Koncopd May 18, 2020
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13 changes: 13 additions & 0 deletions scanpy/tests/test_ingest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,19 @@ def test_neighbors(adatas):
assert percent_correct > 0.99


@pytest.mark.parametrize('n', [3, 4])
def test_neighbors_defaults(adatas, n):
adata_ref = adatas[0].copy()
adata_new = adatas[1].copy()

sc.pp.neighbors(adata_ref, n_neighbors=n)

ing = sc.tl.Ingest(adata_ref)
ing.fit(adata_new)
ing.neighbors()
assert ing._indices.shape[1] == n


@pytest.mark.skipif(
pkg_version("anndata") < sc.tl._ingest.ANNDATA_MIN_VERSION,
reason="`AnnData.concatenate` does not concatenate `.obsm` in old anndata versions",
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11 changes: 8 additions & 3 deletions scanpy/tools/_ingest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,9 +186,11 @@ class Ingest:
"""

def _init_umap(self, adata):
from umap import UMAP
import umap as u

self._umap = UMAP(
u.umap_._HAVE_PYNNDESCENT = False

self._umap = u.UMAP(
metric=self._metric,
random_state=adata.uns['umap']['params'].get('random_state', 0),
)
Expand Down Expand Up @@ -396,7 +398,7 @@ def fit(self, adata_new):
self._adata_new = adata_new
self._obsm['rep'] = self._same_rep()

def neighbors(self, k=10, queue_size=5, random_state=0):
def neighbors(self, k=None, queue_size=5, random_state=0):
"""\
Calculate neighbors of `adata_new` observations in `adata`.

Expand All @@ -412,6 +414,9 @@ def neighbors(self, k=10, queue_size=5, random_state=0):
train = self._rep
test = self._obsm['rep']

if k is None:
k = self._n_neighbors

init = self._initialise_search(
self._rp_forest, train, test, int(k * queue_size), rng_state=rng_state,
)
Expand Down