comparison COBRAxy/marea.py @ 289:3f5cfcf4d9eb draft

Uploaded

288:d1d732d1705c

        reactionId : the provided reaction ID.

    Returns:
        Tuple[str, str]: either a single str ID for the correct arrow head followed by an empty string or both options to try.
    """
    print("getArrowHeadElementId: ", reactionId)
    if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
    elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown:
        print(f"getArrowHeadElementId: {reactionId} this was not unknown.")
        return reactionId[:-3:-1] + reactionId[:-2], "" # ^^^ Invert _F to F_

    return f"F_{reactionId}", f"B_{reactionId}"

class ArrowColor(Enum):
    """
    Encodes possible arrow colors based on their meaning in the enrichment process.
    """
    Invalid       = "#BEBEBE" # gray, fold-change under treshold
    Transparent   = "#ffffff00" # transparent, not significant p-value
    UpRegulated   = "#ecac68" # orange, up-regulated reaction
    DownRegulated = "#6495ed" # lightblue, down-regulated reaction

    UpRegulatedInv = "#FF0000"
    # ^^^ bright red, up-regulated net value for a reversible reaction with

        self.w    = width
        self.col  = col
        self.dash = isDashed
    
    def applyTo(self, reactionId :str, metabMap :ET.ElementTree, styleStr :str) -> None:
        #if 
        getElementById(reactionId, metabMap).map(lambda el : styleMapElement(el, styleStr)).unwrap()
        #.isErr:
        #    ERRORS.append(reactionId)

    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("styleReactionElements: ", idOpt1, idOpt2)
        self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
        if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
    
    # TODO: this seems to be unused, remove
    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
            print("Invalid pValue: ", pValue)
            INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
            continue

        if abs(foldChange) < (ARGS.fChange - 1) / (abs(ARGS.fChange) + 1):
            print("Invalid fc: ", foldChange)
            INVALID_ARROW.styleReactionElements(metabMap, reactionId)
            continue
        
        width = Arrow.MAX_W
        if not math.isinf(foldChange):

289:3f5cfcf4d9eb

        reactionId : the provided reaction ID.

    Returns:
        Tuple[str, str]: either a single str ID for the correct arrow head followed by an empty string or both options to try.
    """
    if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
    elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown:
        return reactionId[:-3:-1] + reactionId[:-2], "" # ^^^ Invert _F to F_

    return f"F_{reactionId}", f"B_{reactionId}"

class ArrowColor(Enum):
    """
    Encodes possible arrow colors based on their meaning in the enrichment process.
    """
    Invalid       = "#BEBEBE" # gray, fold-change under treshold
    UpRegulated   = "#ecac68" # orange, up-regulated reaction
    DownRegulated = "#6495ed" # lightblue, down-regulated reaction

    UpRegulatedInv = "#FF0000"
    # ^^^ bright red, up-regulated net value for a reversible reaction with

        self.w    = width
        self.col  = col
        self.dash = isDashed
    
    def applyTo(self, reactionId :str, metabMap :ET.ElementTree, styleStr :str) -> None:
        if getElementById(reactionId, metabMap).map(lambda el : styleMapElement(el, styleStr)).isErr:
            ERRORS.append(reactionId)

    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)
        self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
        if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
    
    # TODO: this seems to be unused, remove
    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)
            continue
        
        width = Arrow.MAX_W
        if not math.isinf(foldChange):