important fixes

YosefLab · Sep 8, 2024 · 0c177c1 · 0c177c1
1 parent 9e78249
commit 0c177c1
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/tests/test_vivs.py b/tests/test_vivs.py
@@ -39,6 +39,7 @@ def test_jax():
     crttool.train_all()
     crttool.get_importance()
     crttool.get_importance(n_mc_per_pass=10)
+    crttool.get_hier_importance(n_clusters_list=[5, 10])
     crttool.get_cell_scores(gene_ids=[1, 2, 3])
     crttool.get_latent()
 
@@ -53,6 +54,7 @@ def test_jax():
     crttool.train_all()
     crttool.get_importance()
     crttool.get_importance(n_mc_per_pass=10)
+    crttool.get_hier_importance(n_clusters_list=[5, 10])
     crttool.get_cell_scores(gene_ids=[1, 2, 3])
     crttool.get_latent()
 

diff --git a/vivs/_dl_utils.py b/vivs/_dl_utils.py
@@ -32,7 +32,7 @@ def __len__(self):
     def __getitem__(self, idx):
         xmat = self.x_mat[idx]
         if sp.issparse(xmat):
-            xmat = xmat.toarray()
+            xmat = xmat.toarray().squeeze()
         return {
             REGISTRY_KEYS.X_KEY: xmat,
             REGISTRY_KEYS.BATCH_KEY: self.batch_indices[idx],

diff --git a/vivs/_vivs.py b/vivs/_vivs.py
@@ -840,7 +840,7 @@ def plot_hier_importance(
                 )
                 if not are_indices_contiguous:
                     raise ValueError("Gene indices are not contiguous")
-                is_cluster_detected = (res_cluster["padj"] < 0.1).all()
+                is_cluster_detected = (res_cluster["padj"] < significance_threshold).all()
                 if is_cluster_detected:
                     plot_df.append(
                         {