Add seed to leiden clustering (#173)

* Add seed to leiden clustering

* Update _nmi_ari.py

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update test_metrics.py

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update test_metrics.py

* Update test_metrics.py

* Update CHANGELOG.md

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

CHANGELOG.md

@@ -14,6 +14,10 @@ and this project adheres to [Semantic Versioning][].
 
 -   Add `progress_bar` argument to {class}`scib_metrics.benchmark.Benchmarker` {pr}`152`.
 
+### Changed
+
+-   Leiden clustering now has a seed argument for reproducibility {pr}`173`.
+
 ### Fixed
 
 -   Fix neighbors connectivities in test to use new scanpy fn {pr}`170`.

src/scib_metrics/metrics/_nmi_ari.py

@@ -1,4 +1,5 @@
 import logging
+import random
 import warnings
 
 import igraph
@@ -19,7 +20,9 @@ def _compute_clustering_kmeans(X: np.ndarray, n_clusters: int) -> np.ndarray:
     return kmeans.labels_
 
 
-def _compute_clustering_leiden(connectivity_graph: spmatrix, resolution: float) -> np.ndarray:
+def _compute_clustering_leiden(connectivity_graph: spmatrix, resolution: float, seed: int) -> np.ndarray:
+    rng = random.Random(seed)
+    igraph.set_random_number_generator(rng)
     # The connectivity graph with the umap method is symmetric, but we need to first make it directed
     # to have both sets of edges as is done in scanpy. See test for more details.
     g = igraph.Graph.Weighted_Adjacency(connectivity_graph, mode="directed")
@@ -33,8 +36,9 @@ def _compute_nmi_ari_cluster_labels(
     X: spmatrix,
     labels: np.ndarray,
     resolution: float = 1.0,
+    seed: int = 42,
 ) -> tuple[float, float]:
-    labels_pred = _compute_clustering_leiden(X, resolution)
+    labels_pred = _compute_clustering_leiden(X, resolution, seed)
     nmi = normalized_mutual_info_score(labels, labels_pred, average_method="arithmetic")
     ari = adjusted_rand_score(labels, labels_pred)
     return nmi, ari
@@ -71,7 +75,12 @@ def nmi_ari_cluster_labels_kmeans(X: np.ndarray, labels: np.ndarray) -> dict[str
 
 
 def nmi_ari_cluster_labels_leiden(
-    X: NeighborsResults, labels: np.ndarray, optimize_resolution: bool = True, resolution: float = 1.0, n_jobs: int = 1
+    X: NeighborsResults,
+    labels: np.ndarray,
+    optimize_resolution: bool = True,
+    resolution: float = 1.0,
+    n_jobs: int = 1,
+    seed: int = 42,
 ) -> dict[str, float]:
     """Compute nmi and ari between leiden clusters and labels.
 
@@ -93,6 +102,8 @@ def nmi_ari_cluster_labels_leiden(
     n_jobs
         Number of jobs for parallelizing resolution optimization via joblib. If -1, all CPUs
         are used.
+    seed
+        Seed used for reproducibility of clustering.
 
     Returns
     -------
@@ -113,7 +124,7 @@ def nmi_ari_cluster_labels_leiden(
             )
         except ImportError:
             warnings.warn("Using for loop over clustering resolutions. `pip install joblib` for parallelization.")
-            out = [_compute_nmi_ari_cluster_labels(conn_graph, labels, r) for r in resolutions]
+            out = [_compute_nmi_ari_cluster_labels(conn_graph, labels, r, seed=seed) for r in resolutions]
         nmi_ari = np.array(out)
         nmi_ind = np.argmax(nmi_ari[:, 0])
         nmi, ari = nmi_ari[nmi_ind, :]

tests/test_metrics.py

@@ -111,6 +111,16 @@ def test_nmi_ari_cluster_labels_leiden_single_resolution():
     assert isinstance(ari, float)
 
 
+def test_nmi_ari_cluster_labels_leiden_reproducibility():
+    X, labels = dummy_x_labels(symmetric_positive=True, x_is_neighbors_results=True)
+    out1 = scib_metrics.nmi_ari_cluster_labels_leiden(X, labels, optimize_resolution=False, resolution=3.0)
+    out2 = scib_metrics.nmi_ari_cluster_labels_leiden(X, labels, optimize_resolution=False, resolution=3.0)
+    nmi1, ari1 = out1["nmi"], out1["ari"]
+    nmi2, ari2 = out2["nmi"], out2["ari"]
+    assert nmi1 == nmi2
+    assert ari1 == ari2
+
+
 def test_leiden_graph_construction():
     X, _ = dummy_x_labels(symmetric_positive=True, x_is_neighbors_results=True)
     conn_graph = X.knn_graph_connectivities