branch selection robust against NaNs

dpeerlab · May 15, 2024 · 03587b6 · 03587b6
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diff --git a/README.md b/README.md
@@ -53,6 +53,7 @@ Release Notes
 -------------
  ### Version 1.3.4rc
  * avoid devision by zero in `select_branch_cells` for very small datasets
+ * make branch selection robust against NaNs
 
  ### Version 1.3.3
  * optional progress bar with `progress=True` in `palantir.utils.run_local_variability`

diff --git a/src/palantir/presults.py b/src/palantir/presults.py
@@ -546,6 +546,8 @@ def select_branch_cells(
     fate_probs, fate_names = _validate_obsm_key(ad, fate_prob_key, as_df=False)
     pseudotime = ad.obs[pseudo_time_key].values
 
+    fate_probs[np.isnan(fate_probs)] = 1/fate_probs.shape[1]
+
     idx = np.argsort(pseudotime)
     sorted_fate_probs = fate_probs[idx, :]
     prob_thresholds = np.empty_like(fate_probs)