Merge pull request #43 from dpeerlab/issue41

Fix for issue 41
dpeerlab · Sep 3, 2020 · 33aa7fc · 33aa7fc
2 parents 91f301b + a1b20c2
commit 33aa7fc
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 6 deletions.
diff --git a/src/palantir/core.py b/src/palantir/core.py
@@ -316,7 +316,7 @@ def _construct_markov_chain(wp_data, knn, pseudotime, n_jobs):
     # Directed graph construction
     # pseudotime position of all the neighbors
     traj_nbrs = pd.DataFrame(
-        pseudotime[np.ravel(waypoints[ind])].values.reshape(
+        pseudotime[np.ravel(waypoints.values[ind])].values.reshape(
             [len(waypoints), n_neighbors]
         ),
         index=waypoints,

diff --git a/src/palantir/utils.py b/src/palantir/utils.py
@@ -38,11 +38,7 @@ def run_diffusion_maps(data_df, n_components=10, knn=30, alpha=0):
         print("Determing nearest neighbor graph...")
         temp = sc.AnnData(data_df.values)
         sc.pp.neighbors(temp, n_pcs=0, n_neighbors=knn)
-        # maintaining backwards compatibility to Scanpy `sc.pp.neighbors`
-        try:
-            kNN = temp.uns["neighbors"]["distances"]
-        except KeyError:
-            kNN = temp.obsp['distances']
+        kNN = temp.obsp['distances']
 
         # Adaptive k
         adaptive_k = int(np.floor(knn / 3))