Merge branch 'master' into master

chansigit · Jul 12, 2024 · 1d6ba32 · 1d6ba32
2 parents c9fa676 + 26bc5a5
commit 1d6ba32
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/dynamo/plot/preprocess.py b/dynamo/plot/preprocess.py
@@ -915,7 +915,7 @@ def highest_frac_genes(
 
     if gene_annotations is None:
         if gene_annotation_key in adata.var:
-            gene_annotations = adata.var[gene_annotation_key][selected_indices]
+            gene_annotations = adata.var[gene_annotation_key].iloc[selected_indices]
 
         else:
             main_warning(
@@ -930,8 +930,8 @@ def highest_frac_genes(
 
         if gene_annotations is not None:
             ax2 = ax.twiny()
-            ax2.set_xlim(ax.get_ylim())
-            ax2.set_xticks(ax.get_yticks())
+            ax2.set_xlim(ax.get_xlim())
+            ax2.set_xticks(ax.get_xticks())
             ax2.set_xticks(list(range(len(gene_annotations))))
             ax2.set_xticklabels(gene_annotations, rotation=v_rotation, ha="left")
             ax2.set_xlabel(gene_annotation_key)

diff --git a/dynamo/tools/clustering.py b/dynamo/tools/clustering.py
@@ -494,7 +494,7 @@ def cluster_community(
 def cluster_community_from_graph(
     graph=None,
     graph_sparse_matrix: Union[np.ndarray, csr_matrix, None] = None,
-    method: Literal["leiden", "louvain"] = "louvain",
+    method: Literal["leiden", "louvain"] = "leiden",
     directed: bool = False,
     **kwargs
 ) -> Any:

diff --git a/requirements.txt b/requirements.txt
@@ -15,7 +15,7 @@ seaborn>=0.9.0
 colorcet>=2.0.1
 tqdm
 igraph>=0.7.1
-louvain>=0.8.0
+leidenalg
 pynndescent>=0.5.2
 pre-commit
 networkx>=2.6