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comparison COBRAxy/marea.py @ 287:c8622bca2480 draft

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Uploaded
author francesco_lapi
date Wed, 14 May 2025 09:23:52 +0000
parents eaa623b4b703
children d1d732d1705c
comparison
equal deleted inserted replaced
286:eaa623b4b703 287:c8622bca2480
369 reactionId : the provided reaction ID. 369 reactionId : the provided reaction ID.
370 370
371 Returns: 371 Returns:
372 Tuple[str, str]: either a single str ID for the correct arrow head followed by an empty string or both options to try. 372 Tuple[str, str]: either a single str ID for the correct arrow head followed by an empty string or both options to try.
373 """ 373 """
374 print("getArrowHeadElementId: ", reactionId)
374 if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV 375 if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
375 elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown: 376 elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown:
377 print(f"getArrowHeadElementId: {reactionId} this was not unknown.")
376 return reactionId[:-3:-1] + reactionId[:-2], "" # ^^^ Invert _F to F_ 378 return reactionId[:-3:-1] + reactionId[:-2], "" # ^^^ Invert _F to F_
377 379
378 return f"F_{reactionId}", f"B_{reactionId}" 380 return f"F_{reactionId}", f"B_{reactionId}"
379 381
380 class ArrowColor(Enum): 382 class ArrowColor(Enum):
381 """ 383 """
382 Encodes possible arrow colors based on their meaning in the enrichment process. 384 Encodes possible arrow colors based on their meaning in the enrichment process.
383 """ 385 """
384 Invalid = "#BEBEBE" # gray, fold-change under treshold 386 Invalid = "#BEBEBE" # gray, fold-change under treshold
387 Transparent = "#ffffff00" # transparent, not significant p-value
385 UpRegulated = "#ecac68" # orange, up-regulated reaction 388 UpRegulated = "#ecac68" # orange, up-regulated reaction
386 DownRegulated = "#6495ed" # lightblue, down-regulated reaction 389 DownRegulated = "#6495ed" # lightblue, down-regulated reaction
387 390
388 UpRegulatedInv = "#FF0000" 391 UpRegulatedInv = "#FF0000"
389 # ^^^ bright red, up-regulated net value for a reversible reaction with 392 # ^^^ bright red, up-regulated net value for a reversible reaction with
432 if not mindReactionDir: 435 if not mindReactionDir:
433 return self.applyTo(getArrowBodyElementId(reactionId), metabMap, self.toStyleStr()) 436 return self.applyTo(getArrowBodyElementId(reactionId), metabMap, self.toStyleStr())
434 437
435 # Now we style the arrow head(s): 438 # Now we style the arrow head(s):
436 idOpt1, idOpt2 = getArrowHeadElementId(reactionId) 439 idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
440 print("styleReactionElements: ", idOpt1, idOpt2)
437 self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True)) 441 self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
438 if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True)) 442 if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
439 443
440 # TODO: this seems to be unused, remove 444 # TODO: this seems to be unused, remove
441 def getMapReactionId(self, reactionId :str, mindReactionDir :bool) -> str: 445 def getMapReactionId(self, reactionId :str, mindReactionDir :bool) -> str:
494 498
495 if math.isnan(pValue) or (isinstance(foldChange, float) and math.isnan(foldChange)): continue 499 if math.isnan(pValue) or (isinstance(foldChange, float) and math.isnan(foldChange)): continue
496 500
497 if isinstance(foldChange, str): foldChange = float(foldChange) 501 if isinstance(foldChange, str): foldChange = float(foldChange)
498 if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow 502 if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
503 print("Invalid pValue: ", pValue)
499 INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId) 504 INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
500 continue 505 continue
501 506
502 if abs(foldChange) < (ARGS.fChange - 1) / (abs(ARGS.fChange) + 1): 507 if abs(foldChange) < (ARGS.fChange - 1) / (abs(ARGS.fChange) + 1):
508 print("Invalid fc: ", foldChange)
503 INVALID_ARROW.styleReactionElements(metabMap, reactionId) 509 INVALID_ARROW.styleReactionElements(metabMap, reactionId)
504 continue 510 continue
505 511
506 width = Arrow.MAX_W 512 width = Arrow.MAX_W
507 if not math.isinf(foldChange): 513 if not math.isinf(foldChange):