Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_to_map.py @ 275:e87aeb3a33cd draft

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author francesco_lapi
date Mon, 05 May 2025 10:33:06 +0000
parents d54d6728b204
children
comparison
equal deleted inserted replaced
274:d54d6728b204 275:e87aeb3a33cd
260 tmp = d.get(el_id[2:]) 260 tmp = d.get(el_id[2:])
261 if tmp != None: 261 if tmp != None:
262 p_val :float = tmp[0] 262 p_val :float = tmp[0]
263 f_c = tmp[1] 263 f_c = tmp[1]
264 z_score = tmp[2] 264 z_score = tmp[2]
265
266 if math.isnan(p_val) or (isinstance(f_c, float) and math.isnan(f_c)): continue
267
265 if p_val < threshold_P_V: 268 if p_val < threshold_P_V:
266 if not isinstance(f_c, str): 269 if not isinstance(f_c, str):
267 if abs(f_c) < ((threshold_F_C - 1) / (abs(threshold_F_C) + 1)): # 270 if abs(f_c) < ((threshold_F_C - 1) / (abs(threshold_F_C) + 1)): #
268 col = grey 271 col = grey
269 width = str(minT) 272 width = str(minT)
474 for reactionId, values in fluxesEnrichmentRes.items(): 477 for reactionId, values in fluxesEnrichmentRes.items():
475 pValue = values[0] 478 pValue = values[0]
476 foldChange = values[1] 479 foldChange = values[1]
477 z_score = values[2] 480 z_score = values[2]
478 481
482 if math.isnan(pValue) or (isinstance(foldChange, float) and math.isnan(foldChange)):
483 continue
484
479 if isinstance(foldChange, str): foldChange = float(foldChange) 485 if isinstance(foldChange, str): foldChange = float(foldChange)
480 if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow 486 if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
481 INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId) 487 INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
482 INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId, mindReactionDir = False) 488 INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId, mindReactionDir = False)
483 489
724 try: 730 try:
725 p_value, z_score = computePValue(l1, l2) 731 p_value, z_score = computePValue(l1, l2)
726 avg1 = sum(l1) / len(l1) 732 avg1 = sum(l1) / len(l1)
727 avg2 = sum(l2) / len(l2) 733 avg2 = sum(l2) / len(l2)
728 f_c = fold_change(avg1, avg2) 734 f_c = fold_change(avg1, avg2)
729 if math.isnan(p_value) or (isinstance(f_c, float) and math.isnan(f_c)): continue
730 if not isinstance(z_score, str) and max_z_score < abs(z_score): max_z_score = abs(z_score) 735 if not isinstance(z_score, str) and max_z_score < abs(z_score): max_z_score = abs(z_score)
731 736
732 tmp[reactId] = [float(p_value), f_c, z_score, avg1, avg2] 737 tmp[reactId] = [float(p_value), f_c, z_score, avg1, avg2]
733 except (TypeError, ZeroDivisionError): continue 738 except (TypeError, ZeroDivisionError): continue
734 739