Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_to_map.py @ 295:626b6d1de075 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author francesco_lapi
date Fri, 16 May 2025 10:56:01 +0000
parents 7b8d9de81a86
children 753347af8bc9
comparison
equal deleted inserted replaced
294:274223ff4fb0 295:626b6d1de075
63 parser.add_argument( 63 parser.add_argument(
64 '-pv' ,'--pValue', 64 '-pv' ,'--pValue',
65 type = float, 65 type = float,
66 default = 0.1, 66 default = 0.1,
67 help = 'P-Value threshold (default: %(default)s)') 67 help = 'P-Value threshold (default: %(default)s)')
68
69 parser.add_argument(
70 '-adj' ,'--adjusted',
71 type = utils.Bool("adjusted"), default = False,
72 help = 'Apply the FDR (Benjamini-Hochberg) correction (default: %(default)s)')
68 73
69 parser.add_argument( 74 parser.add_argument(
70 '-fc', '--fChange', 75 '-fc', '--fChange',
71 type = float, 76 type = float,
72 default = 1.5, 77 default = 1.5,
73 help = 'Fold-Change threshold (default: %(default)s)') 78 help = 'Fold-Change threshold (default: %(default)s)')
74 79
75
76 parser.add_argument( 80 parser.add_argument(
77 '-op', '--option', 81 '-op', '--option',
78 type = str, 82 type = str,
79 choices = ['datasets', 'dataset_class'], 83 choices = ['datasets', 'dataset_class'],
80 help='dataset or dataset and class') 84 help='dataset or dataset and class')
647 651
648 return p_value, z_score 652 return p_value, z_score
649 653
650 def compareDatasetPair(dataset1Data :List[List[float]], dataset2Data :List[List[float]], ids :List[str]) -> Tuple[Dict[str, List[Union[float, FoldChange]]], float]: 654 def compareDatasetPair(dataset1Data :List[List[float]], dataset2Data :List[List[float]], ids :List[str]) -> Tuple[Dict[str, List[Union[float, FoldChange]]], float]:
651 #TODO: the following code still suffers from "dumbvarnames-osis" 655 #TODO: the following code still suffers from "dumbvarnames-osis"
652 tmp :Dict[str, List[Union[float, FoldChange]]] = {} 656 comparisonResult :Dict[str, List[Union[float, FoldChange]]] = {}
653 count = 0 657 count = 0
654 max_z_score = 0 658 max_z_score = 0
655 for l1, l2 in zip(dataset1Data, dataset2Data): 659 for l1, l2 in zip(dataset1Data, dataset2Data):
656 reactId = ids[count] 660 reactId = ids[count]
657 count += 1 661 count += 1
662 avg1 = sum(l1) / len(l1) 666 avg1 = sum(l1) / len(l1)
663 avg2 = sum(l2) / len(l2) 667 avg2 = sum(l2) / len(l2)
664 f_c = fold_change(avg1, avg2) 668 f_c = fold_change(avg1, avg2)
665 if np.isfinite(z_score) and max_z_score < abs(z_score): max_z_score = abs(z_score) 669 if np.isfinite(z_score) and max_z_score < abs(z_score): max_z_score = abs(z_score)
666 670
667 tmp[reactId] = [float(p_value), f_c, z_score, avg1, avg2] 671 comparisonResult[reactId] = [float(p_value), f_c, z_score, avg1, avg2]
668 except (TypeError, ZeroDivisionError): continue 672 except (TypeError, ZeroDivisionError): continue
669 673
670 return tmp, max_z_score 674 # Apply multiple testing correction if set by the user
675 if ARGS.adjusted:
676
677 # Retrive the p-values from the comparisonResult dictionary
678 reactIds = list(comparisonResult.keys())
679 pValues = [comparisonResult[reactId][0] for reactId in reactIds]
680
681 # Apply the Benjamini-Hochberg correction and update
682 adjustedPValues = st.multipletests(pValues, method="fdr_bh")[1]
683 for i, reactId in enumerate(reactIds):
684 comparisonResult[reactId][0] = adjustedPValues[i]
685
686 return comparisonResult, max_z_score
671 687
672 def computeEnrichment(class_pat :Dict[str, List[List[float]]], ids :List[str]) -> List[Tuple[str, str, dict, float]]: 688 def computeEnrichment(class_pat :Dict[str, List[List[float]]], ids :List[str]) -> List[Tuple[str, str, dict, float]]:
673 """ 689 """
674 Compares clustered data based on a given comparison mode and applies enrichment-based styling on the 690 Compares clustered data based on a given comparison mode and applies enrichment-based styling on the
675 provided metabolic map. 691 provided metabolic map.