added small eps to np.log

goodarzilab · Apr 30, 2024 · 1867251 · 1867251
1 parent 8b436f6
commit 1867251
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/pypage/page.py b/pypage/page.py
@@ -355,8 +355,8 @@ def _gather_results(self) -> pd.DataFrame:
         """Gathers the results from the experiment into a single dataframe
         """
         # estimate sign
-        self.log_overrep_pvals = np.log10(self.overrep_pvals)
-        self.log_underrep_pvals = np.log10(self.underrep_pvals)
+        self.log_overrep_pvals = np.log10(self.overrep_pvals + 1e-8)
+        self.log_underrep_pvals = np.log10(self.underrep_pvals + 1e-8)
         self.graphical_ar = np.minimum(self.log_overrep_pvals, self.log_underrep_pvals)
         self.graphical_ar[self.log_overrep_pvals < self.log_underrep_pvals] *= -1  # make overrepresented positive
         n_bins = self.graphical_ar.shape[1]
@@ -455,4 +455,4 @@ def get_es_matrix(self):
         return pd.DataFrame(
             hm._subset_and_sort_pathways()[1],
             index=hm._subset_and_sort_pathways()[0]
-        )
+        )