Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_to_map.py @ 211:4e368ecd4fb6 draft

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author francesco_lapi
date Thu, 28 Nov 2024 15:41:30 +0000
parents df664d1a86d4
children ba7043091fe3
comparison
equal deleted inserted replaced
210:3ca179b83574 211:4e368ecd4fb6
725 p_value, z_score = computePValue(l1, l2) 725 p_value, z_score = computePValue(l1, l2)
726 avg1 = sum(l1) / len(l1) 726 avg1 = sum(l1) / len(l1)
727 avg2 = sum(l2) / len(l2) 727 avg2 = sum(l2) / len(l2)
728 f_c = fold_change(avg1, avg2) 728 f_c = fold_change(avg1, avg2)
729 if not isinstance(z_score, str) and max_z_score < abs(z_score): max_z_score = abs(z_score) 729 if not isinstance(z_score, str) and max_z_score < abs(z_score): max_z_score = abs(z_score)
730 print(reactId, 'pValue ', float(p_value), 'fold change ', f_c, 'z_score ', z_score, 'avg1 ', avg1, 'avg2 ', avg2) 730
731 tmp[reactId] = [float(p_value), f_c, z_score, avg1, avg2] 731 tmp[reactId] = [float(p_value), f_c, z_score, avg1, avg2]
732 except (TypeError, ZeroDivisionError): continue 732 except (TypeError, ZeroDivisionError): continue
733 733
734 return tmp, max_z_score 734 return tmp, max_z_score
735 735
757 enrichment_results = [] 757 enrichment_results = []
758 758
759 759
760 if ARGS.comparison == "manyvsmany": 760 if ARGS.comparison == "manyvsmany":
761 for i, j in it.combinations(class_pat.keys(), 2): 761 for i, j in it.combinations(class_pat.keys(), 2):
762 print(f"Comparing {i} and {j}") 762
763 comparisonDict, max_z_score = compareDatasetPair(class_pat.get(i), class_pat.get(j), ids) 763 comparisonDict, max_z_score = compareDatasetPair(class_pat.get(i), class_pat.get(j), ids)
764 enrichment_results.append((i, j, comparisonDict, max_z_score)) 764 enrichment_results.append((i, j, comparisonDict, max_z_score))
765 765
766 elif ARGS.comparison == "onevsrest": 766 elif ARGS.comparison == "onevsrest":
767 for single_cluster in class_pat.keys(): 767 for single_cluster in class_pat.keys():
768 rest = [item for k, v in class_pat.items() if k != single_cluster for item in v] 768 rest = [item for k, v in class_pat.items() if k != single_cluster for item in v]
769 print(f"Comparing {single_cluster} and {rest}") 769
770 comparisonDict, max_z_score = compareDatasetPair(class_pat.get(single_cluster), rest, ids) 770 comparisonDict, max_z_score = compareDatasetPair(class_pat.get(single_cluster), rest, ids)
771 enrichment_results.append((single_cluster, "rest", comparisonDict, max_z_score)) 771 enrichment_results.append((single_cluster, "rest", comparisonDict, max_z_score))
772 772
773 elif ARGS.comparison == "onevsmany": 773 elif ARGS.comparison == "onevsmany":
774 controlItems = class_pat.get(ARGS.control) 774 controlItems = class_pat.get(ARGS.control)