Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_to_map.py @ 197:1306b3543e57 draft

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Uploaded
author francesco_lapi
date Thu, 21 Nov 2024 10:43:48 +0000
parents 8b7d2e6b4995
children 1dda40a60037
comparison
equal deleted inserted replaced
196:07539860dbca 197:1306b3543e57
495 width = max(abs(z_score * Arrow.MAX_W) / maxNumericZScore, Arrow.MIN_W) 495 width = max(abs(z_score * Arrow.MAX_W) / maxNumericZScore, Arrow.MIN_W)
496 496
497 except ZeroDivisionError: pass 497 except ZeroDivisionError: pass
498 # TODO CHECK RV 498 # TODO CHECK RV
499 #if not reactionId.endswith("_RV"): # RV stands for reversible reactions 499 #if not reactionId.endswith("_RV"): # RV stands for reversible reactions
500 # Arrow(width, ArrowColor.fromFoldChangeSign(foldChange)).styleReactionElements(metabMap, reactionId) 500 # Arrow(width, ArrowColor.fromFoldChangeSign(foldChange)).styleReactionElements(metabMap, reactionId)
501 # continue 501 # continue
502 502
503 #reactionId = reactionId[:-3] # Remove "_RV" 503 #reactionId = reactionId[:-3] # Remove "_RV"
504 504
505 inversionScore = (values[3] < 0) + (values[4] < 0) # Compacts the signs of averages into 1 easy to check score 505 inversionScore = (values[3] < 0) + (values[4] < 0) # Compacts the signs of averages into 1 easy to check score
506 if inversionScore == 2: foldChange *= -1 506 if inversionScore == 2: foldChange *= -1
724 724
725 try: 725 try:
726 p_value, z_score = computePValue(l1, l2) 726 p_value, z_score = computePValue(l1, l2)
727 avg1 = sum(l1) / len(l1) 727 avg1 = sum(l1) / len(l1)
728 avg2 = sum(l2) / len(l2) 728 avg2 = sum(l2) / len(l2)
729 avg = fold_change(avg1, avg2) 729 f_c = fold_change(avg1, avg2)
730 if not isinstance(z_score, str) and max_z_score < abs(z_score): max_z_score = abs(z_score) 730 if not isinstance(z_score, str) and max_z_score < abs(z_score): max_z_score = abs(z_score)
731 tmp[reactId] = [float(p_value), avg, z_score, avg1, avg2] 731 print(reactId, float(p_value), f_c, z_score, avg1, avg2)
732 tmp[reactId] = [float(p_value), f_c, z_score, avg1, avg2]
732 except (TypeError, ZeroDivisionError): continue 733 except (TypeError, ZeroDivisionError): continue
733 734
734 return tmp, max_z_score 735 return tmp, max_z_score
735 736
736 def computeEnrichment(class_pat :Dict[str, List[List[float]]], ids :List[str]) -> List[Tuple[str, str, dict, float]]: 737 def computeEnrichment(class_pat :Dict[str, List[List[float]]], ids :List[str]) -> List[Tuple[str, str, dict, float]]: