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Converts NaNs in pval to 1s (#365)

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Charlotte Weaver
2018-10-24 10:57:29 -07:00
committed by GitHub
parent 7aa390b5a1
commit 85f44ccabf
1 changed files with 10 additions and 1 deletions
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server/app/scanpy_engine/scanpy_engine.py
+10 -1
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@@ -94,6 +94,15 @@ class ScanpyEngine(CXGDriver):
""" """
return values[sort_order][:top_n] return values[sort_order][:top_n]
@staticmethod
def _nan_to_one(values):
"""
Replaces NaN values with 1
:param values: numpy ndarray
:return: ndarray
"""
return np.where(np.isnan(values), 1, values)
def _add_mandatory_annotations(self): def _add_mandatory_annotations(self):
# ensure gene # ensure gene
self.data.var["name"] = Series(list(self.data.var.index), dtype="unicode_", index=self.data.var.index) self.data.var["name"] = Series(list(self.data.var.index), dtype="unicode_", index=self.data.var.index)
@@ -300,7 +309,7 @@ class ScanpyEngine(CXGDriver):
genes_idx = df1.var.index genes_idx = df1.var.index
diffexp_result = stats.ttest_ind(df1.X, df2.X) diffexp_result = stats.ttest_ind(df1.X, df2.X)
pval = diffexp_result.pvalue pval = self._nan_to_one(diffexp_result.pvalue)
bonferroni_pval = 1 - (1 - pval) ** self.gene_count bonferroni_pval = 1 - (1 - pval) ** self.gene_count
ave_exp_set1 = np.mean(df1.X, axis=0) ave_exp_set1 = np.mean(df1.X, axis=0)
ave_exp_set2 = np.mean(df2.X, axis=0) ave_exp_set2 = np.mean(df2.X, axis=0)