fix ep.tl.umap when neighbors_key is not None (#790)

* remove buggy extra uns checks of ep, let sc do it * add check with ep instruction * Update ehrapy/tools/_scanpy_tl_api.py Co-authored-by: Lukas Heumos <[email protected]> --------- Co-authored-by: Lukas Heumos <[email protected]>
theislab · Aug 23, 2024 · 423a633 · 423a633
1 parent 4e48886
commit 423a633
Showing 1 changed file with 22 additions and 20 deletions.
diff --git a/ehrapy/tools/_scanpy_tl_api.py b/ehrapy/tools/_scanpy_tl_api.py
@@ -159,26 +159,28 @@ def umap(
 
         **X_umap** : `adata.obsm` field UMAP coordinates of data.
     """
-    if adata.uns["neighbors"] is None or neighbors_key not in adata.uns:
-        return sc.tl.umap(
-            adata=adata,
-            min_dist=min_dist,
-            spread=spread,
-            n_components=n_components,
-            maxiter=maxiter,
-            alpha=alpha,
-            gamma=gamma,
-            negative_sample_rate=negative_sample_rate,
-            init_pos=init_pos,
-            random_state=random_state,
-            a=a,
-            b=b,
-            copy=copy,
-            method=method,
-            neighbors_key=neighbors_key,
-        )
-    else:
-        raise ValueError(f'.uns["{neighbors_key}"] or .uns["neighbors"] were not found. Run `ep.pp.neighbors` first.')
+
+    key_to_check = neighbors_key if neighbors_key is not None else "neighbors"
+    if key_to_check not in adata.uns:
+        raise ValueError(f"Did not find .uns[{key_to_check!r}]. Please run `ep.pp.neighbors` first.")
+
+    return sc.tl.umap(
+        adata=adata,
+        min_dist=min_dist,
+        spread=spread,
+        n_components=n_components,
+        maxiter=maxiter,
+        alpha=alpha,
+        gamma=gamma,
+        negative_sample_rate=negative_sample_rate,
+        init_pos=init_pos,
+        random_state=random_state,
+        a=a,
+        b=b,
+        copy=copy,
+        method=method,
+        neighbors_key=neighbors_key,
+    )
 
 
 def draw_graph(