do not plot nan cluster

dpeerlab · May 15, 2024 · 30046bc · 30046bc
1 parent 66971d4
commit 30046bc
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diff --git a/README.md b/README.md
@@ -54,6 +54,7 @@ Release Notes
  ### Version 1.3.4rc
  * avoid devision by zero in `select_branch_cells` for very small datasets
  * make branch selection robust against NaNs
+ * do not plot unclustered trends (NaN cluster) in `plot_gene_trend_clusters`
 
  ### Version 1.3.3
  * optional progress bar with `progress=True` in `palantir.utils.run_local_variability`

diff --git a/notebooks/Palantir_sample_notebook.ipynb b/notebooks/Palantir_sample_notebook.ipynb
diff --git a/src/palantir/plot.py b/src/palantir/plot.py
@@ -1748,10 +1748,12 @@ def plot_gene_trend_clusters(
 
     # Obtain unique clusters and prepare figure
     cluster_labels = (
-        clusters.cat.categories
+        set(clusters.cat.categories)
         if isinstance(clusters, pd.CategoricalDtype)
         else set(clusters)
     )
+    cluster_labels = cluster_labels.difference({np.NaN})
+
     n_rows = int(np.ceil(len(cluster_labels) / 3))
     fig = plt.figure(figsize=[5.5 * 3, 2.5 * n_rows])