comparison COBRAxy/marea.py @ 283:2436856c7e51 draft

Uploaded

282:f5635309779a

    def styleReactionElements(self, metabMap :ET.ElementTree, reactionId :str, *, mindReactionDir = True) -> None:
        # If We're dealing with RAS data or in general don't care about the direction of the reaction we only style the arrow body
        if not mindReactionDir:
            return self.applyTo(getArrowBodyElementId(reactionId), metabMap, self.toStyleStr())
        print('PROVA 1')
        # Now we style the arrow head(s):
        idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
        self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
        if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
    
    def getMapReactionId(self, reactionId :str, mindReactionDir :bool) -> str:
        """

        if math.isnan(pValue) or (isinstance(foldChange, float) and math.isnan(foldChange)): continue

        if isinstance(foldChange, str): foldChange = float(foldChange)
        if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
            INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
            print('PROVA 2')
            continue

        if abs(foldChange) <  (ARGS.fChange - 1) / (abs(ARGS.fChange) + 1):
            INVALID_ARROW.styleReactionElements(metabMap, reactionId)
            continue
        
        width = Arrow.MAX_W
        if not math.isinf(foldChange):
            try: width = max(abs(z_score * Arrow.MAX_W) / maxNumericZScore, Arrow.MIN_W)

        # If the score is 1 (opposite signs) we use alternative colors vvv
        arrow = Arrow(width, ArrowColor.fromFoldChangeSign(foldChange, useAltColor = inversionScore == 1))
        
        # vvv These 2 if statements can both be true and can both happen
        if ARGS.net: # style arrow head(s):
            arrow.styleReactionElements(metabMap, reactionId + ("_B" if inversionScore == 2 else "_F"))
        
        if not ARGS.using_RAS: # style arrow body
            arrow.styleReactionElements(metabMap, reactionId, mindReactionDir = False)

283:2436856c7e51

    def styleReactionElements(self, metabMap :ET.ElementTree, reactionId :str, *, mindReactionDir = True) -> None:
        # If We're dealing with RAS data or in general don't care about the direction of the reaction we only style the arrow body
        if not mindReactionDir:
            return self.applyTo(getArrowBodyElementId(reactionId), metabMap, self.toStyleStr())
        # Now we style the arrow head(s):
        idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
        print(f'{idOpt1} {self.toStyleStr(downSizedForTips = True)}')
        if idOpt2: print(f'{idOpt2} {self.toStyleStr(downSizedForTips = True)}')
        print('----')
        self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
        if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
    
    def getMapReactionId(self, reactionId :str, mindReactionDir :bool) -> str:
        """

        if math.isnan(pValue) or (isinstance(foldChange, float) and math.isnan(foldChange)): continue

        if isinstance(foldChange, str): foldChange = float(foldChange)
        if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
            INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
            continue

        if abs(foldChange) <  (ARGS.fChange - 1) / (abs(ARGS.fChange) + 1):
            INVALID_ARROW.styleReactionElements(metabMap, reactionId)
            print('Prova 2')
            continue
        
        width = Arrow.MAX_W
        if not math.isinf(foldChange):
            try: width = max(abs(z_score * Arrow.MAX_W) / maxNumericZScore, Arrow.MIN_W)

        # If the score is 1 (opposite signs) we use alternative colors vvv
        arrow = Arrow(width, ArrowColor.fromFoldChangeSign(foldChange, useAltColor = inversionScore == 1))
        
        # vvv These 2 if statements can both be true and can both happen
        if ARGS.net: # style arrow head(s):
            print('Prova NET')
            arrow.styleReactionElements(metabMap, reactionId + ("_B" if inversionScore == 2 else "_F"))
        
        if not ARGS.using_RAS: # style arrow body
            arrow.styleReactionElements(metabMap, reactionId, mindReactionDir = False)