update

gisea/run.py

@@ -0,0 +1,39 @@
+import pandas as pd
+import igraph as ig
+from time import time
+import blitzgsea
+
+
+def runGISEA(mat, library, processes=6):
+    t0 = time()
+    print("runGISEA...")
+
+    FullResults = {}
+
+    for i, _ in enumerate(mat.index):
+        signature = mat.iloc[i, :].reset_index()
+        gene_name = mat.index[i]
+
+        result = blitzgsea.gsea(signature, library, processes=processes)
+
+        FullResults[gene_name] = result.to_dict()
+        del result, signature
+
+    print("done in %0.3fs" % (time() - t0))
+    return FullResults
+
+
+def gsea_to_matrix(results, info, obs_dict, pivot=True):
+    """
+    'es', 'nes', 'pval', 'sidak', 'fdr', 'geneset_size', 'leading_edge', 'leading_edge_size'
+    """
+    mat = [(obs, term, val) for obs in results for term, val in results[obs][info].items()]
+    mat = pd.DataFrame(mat, columns=['Gene', 'Term', info])
+    if pivot:
+        mat = mat.pivot(index=['Gene'], columns=['Term'], values=info)
+    mat.columns.name = None
+
+    mat = mat.loc[obs_dict.keys(),]
+    mat.index = obs_dict.values()
+
+    return mat