Merge pull request #24 from SBRG/devel

Improved pathway visualization

Toolbox/Core.m

@@ -1421,9 +1421,9 @@
 balancing=Thread[Rule[model["Reactions"],Expand/@((model["Species"]/.Dispatch[updateRules[model["ElementalComposition"],OptionValue["ElementalComposition"]]]).model)]];
 balancing=DeleteCases[balancing,r_Rule/;MemberQ[exclude,r[[1]]]];
 If[
-Total[balancing[[All,2]]]==0,
+Round[Total[balancing[[All,2]]]]===0.,
 True,
-Message[elementallyBalancedQ::notBalanced,SlideView[Rule@@@Cases[balancing,r_Rule/;r[[2]]=!=0]]];False]
+Message[elementallyBalancedQ::notBalanced,SlideView[Rule@@@Cases[balancing,r_Rule/;Round[r[[2]]]=!=0],AppearanceElements->All]];False]
 ];
 def:elementallyBalancedQ[___]:=(Message[Toolbox::badargs,elementallyBalancedQ,Defer@def];Abort[])
 Protect[elementallyBalancedQ];

Toolbox/Types.m

@@ -97,12 +97,15 @@
 
 Unprotect[formula2elementalComposition];
 Options[formula2elementalComposition]=Options[elementalComposition2formula];
-formula2elementalComposition[formula_String,opts:OptionsPattern[]]:=Module[{tmp},
-	tmp=Sort[StringCases[StringReplace[formula,RegularExpression[OptionValue["EscapingCharacter"]<>".*?"<>OptionValue["EscapingCharacter"]<>"\\d*"]->""],RegularExpression["([\\D^"<>OptionValue["EscapingCharacter"]<>"]{1})(\\d*)"]:>Rule["$1",ToExpression["$2"/.""->"1"]]]];
-	If[OptionValue["PseudoElements"]===True,
-		tmp=Join[tmp,StringCases[formula,RegularExpression["("<>OptionValue["EscapingCharacter"]<>".+?"<>OptionValue["EscapingCharacter"]<>")"<>"(\\d*)"]:>Rule["$1",ToExpression["$2"/.""->"1"]]]]
+formula2elementalComposition[formula_String,opts:OptionsPattern[]]:=Module[{tmp,elems=chemicalElements,realElements,weirdElements},
+	realElements=StringCases[formula,RegularExpression["("<>StringJoin@@Riffle[Join[Reverse@SortBy[elems,StringLength],{OptionValue["EscapingCharacter"]<>".*?"<>OptionValue["EscapingCharacter"]}],"|"]<>")(\\d*)"]:>Rule["$1",ToExpression["$2"/.""->"1"]]];
+	If[OptionValue["PseudoElements"],
+		weirdElements=OptionValue["EscapingCharacter"]<>#[[1]]<>OptionValue["EscapingCharacter"]->#[[2]]&/@Complement[StringCases[formula,RegularExpression["("<>StringJoin@@Riffle[Join[Reverse@SortBy[elems,StringLength],{OptionValue["EscapingCharacter"]<>".*?"<>OptionValue["EscapingCharacter"],"\\D"}],"|"]<>")(\\d*)"]:>Rule["$1",ToExpression["$2"/.""->"1"]]],realElements];,
+		weirdElements={};
 	];
-	Plus@@Times@@@tmp
+
+	tmp=Sort[Join[realElements,weirdElements]];
+	tmp=Plus@@Times@@@tmp
 ];
 def:formula2elementalComposition[___]:=(Message[Toolbox::badargs,formula2elementalComposition,Defer@def];Abort[])
 Protect[formula2elementalComposition];
@@ -492,8 +495,9 @@
 
 
 Unprotect[complementParameters];
-complementParameters[param:{Rule[(_rateconst|_Keq|metabolite[_,"Xt"]|_parameter),_]..}]:=Module[{ids,completeSet},
+complementParameters[param:{_Rule...}]:=Module[{ids,completeSet},
 	ids=Union[getID/@DeleteCases[param[[All,1]],Append[$MASS$speciesPattern,_parameter]]];
+	If[ids==={},Return[param]]; (*Nothing to complement ...*)
 	completeSet=Thread[Rule[#,#]]&@Flatten[Transpose[Table[{rateconst[i,True],rateconst[i,False],Keq[i]},{i,ids}]]];
 	Join[
 		FixedPoint[#/.{Rule[a_Keq,b_]:>(a->keq2k[b/.param]),Rule[a:rateconst[_,True],b_]:>(a->kFwd2keq[b/.param]),Rule[a:rateconst[_,False],b_]:>(a->k2keq[b/.param])}&,completeSet],

Toolbox/Visualization.m

@@ -419,15 +419,44 @@
 Protect[drawReactionMap];
 
 
+$SimphenyInternalIDsToNames={"252134"->"iMM904_COMBINED","294177"->"iJR904_Alternate_Carbon_Sources","133267"->"iJR904_Amino_Acid_Metabolism","225959"->"iJR904_Cell_Membrane_Constituents","224016"->"iJR904_Central_Metabolism","303020"->"iJR904_Cofactor_Biosynthesis","305120"->"iJR904_Nucleotide_Metabolism","234509"->"iJR904_COMBINED","1226614"->"iAF1260_Alternate_Carbon_Sources","1230565"->"iAF1260_Amino_Acid_Metabolism","1555394"->"iAF1260_Central_Metabolism","1240422"->"iAF1260_Cofactor_Biosynthesis","1233958"->"iAF1260_Fatty_Acid_Biosynthesis","861115"->"iAF1260_Inorganic_Ion_Transport_(Inner_Membrane)","1243392"->"iAF1260_Lipopolysaccharide_(LPS)_Biosynthesis","651224"->"iAF1260_Murein_Biosynthesis_and_Recycling","1237864"->"iAF1260_Nucleotide_Metabolism","1225142"->"iAF1260_tRNA_Charging","1276939"->"iAF1260_COMBINED","745364"->"Recon1_AMINO_ACID_METABOLISM","607474"->"Recon1_CARBOHYDRATE_METABOLISM","854888"->"Recon1_ENERGY_METABOLISM","681892"->"Recon1_GLYCAN_METABOLISM","1103958"->"Recon1_LIPID_METABOLISM","700994"->"Recon1_NUCLEOTIDE_METABOLISM","821108"->"Recon1_SECONDARY_METABOLITES","851235"->"Recon1_VITAMIN_&_COFACTOR_METABOLISM","1014133"->"Recon1_COMBINED","22199"->"iND750_Amino_Acid_Metabolism","35089"->"iND750_Cofactor_and_Vitamin_Biosynthesis","38537"->"iND750_Lipid_Metabolism","20179"->"iND750_Nucleotide_Metabolism","666364"->"iND750_COMBINED","382379"->"iAF692_Vitamin_and_Cofactor_Biosynthesis","441083"->"iAF692_Nucleotide_Metabolism","447592"->"iAF692_COMBINED","549"->"iIT341_Central_Metabolism","503671"->"iIT341_Co-set_Order","387841"->"iIT341_COMBINED","340794"->"iSB619_Amino_Acid_Metabolism","340815"->"iSB619_Biomass","340795"->"iSB619_Central_Metabolism","340806"->"iSB619_Cofactor_Biosynthesis","385801"->"iSB619_Heme_Biosynthesis","340797"->"iSB619_Oxidative_Phosphorylation","340798"->"iSB619_Pentose_Phosphate","340800"->"iSB619_Purine/Pyrimidine_Metabolism","390808"->"iSB619_COMBINED","1576807"->"EcoliCore_coreMap","1148996"->"iNJ661_COMBINED"};
+$AVAILABLEMAPS=StringSplit[FileNameSplit[#][[-1]],"_"][[1]]->#&/@FileNames["*.gz",{FileNameJoin[{$ToolboxPath,"maps","bigg_maps"}]}];
+$AVAILABLEMAPS=$AVAILABLEMAPS/.$SimphenyInternalIDsToNames;
+
+
 Unprotect[drawPathway];
-Options[drawPathway]={"PlotLegends"->None,"Tooltips"->True,"ColorFunctionScaling"->True,"Boundary"->True,"ReactionData"->{},"MetaboliteData"->{},ColorFunction->ColorData["Rainbow"],"MinSize"->0.005,"MaxSize"->0.01,"MinThickness"->0.001,"MaxThickness"->0.003,"TextStyle"->{FontFamily->"Arial",FontSize->Scaled[.008]},"MetaboliteStyle"->Options[drawMetaboliteMap],"ReactionStyle"->Options[drawReactionMap],ImageSize->350};
-drawPathway[metPos:{_Rule..},rxnPos:{_Rule..},textPos:({(_Text|_Rule|_Style)..}|{}),opts:OptionsPattern[{drawPathway,drawReactionMap,drawMetaboliteMap}]]:=Module[{map,fluxStyle,metStyle,cellMembrane,corners,aspectRatio,cleanRxnData,scalingFunction,cleanMetaboliteData},
-	scalingFunction=Switch[OptionValue["ColorFunctionScaling"],True,Rescale[Abs@#,{Min[Abs@#],Max[Abs@#]},{0.,1.}]&,_Function,OptionValue["ColorFunctionScaling"],False,#&];
+Options[drawPathway]={"MinMaxHack"->False,"PlotLegends"->None,"Tooltips"->True,"ColorFunctionScaling"->True,"Boundary"->False,"ReactionData"->{},"MetaboliteData"->{},ColorFunction->ColorData["Rainbow"],"MinSize"->0.005,"MaxSize"->0.01,"MinThickness"->0.001,"MaxThickness"->0.003,"TextStyle"->{FontFamily->"Arial",FontSize->Scaled[.008]},"MetaboliteStyle"->Options[drawMetaboliteMap],"ReactionStyle"->Options[drawReactionMap],ImageSize->350};
+drawPathway::unknowmap="Map `1` is not available. Try drawPathway[] to see a list of available maps";
+drawPathway[]:=Sort[$AVAILABLEMAPS[[All,1]]]
+drawPathway[mapID_String,opts:OptionsPattern[{drawPathway,drawReactionMap,drawMetaboliteMap}]]:=Module[{cmpdPos,rxnPos,finalLabels,mapData},
+	If[MemberQ[$AVAILABLEMAPS[[All,1]],mapID], mapData=Import[mapID/.$AVAILABLEMAPS], Message[drawPathway,mapID];Abort[];];
+	cmpdPos=Flatten[query["cmpd_pos",mapData,{}]];
+	rxnPos=query["rxn_pos",mapData];
+	finalLabels={};
+	drawPathway[cmpdPos,rxnPos,finalLabels,opts]
+];
+drawPathway[metPos:{_Rule..},rxnPos:{_Rule..},textPos:({(_Text|_Rule|_Style)..}|{}),opts:OptionsPattern[{drawPathway,drawReactionMap,drawMetaboliteMap}]]:=Module[{refMin,refMax,helperFunc,min,max,directedQ,map,fluxStyle,metStyle,cellMembrane,corners,aspectRatio,cleanRxnData,scalingFunction,cleanMetaboliteData},
+	directedQ="Directed"/.(ToString[#[[1]]]->#[[2]]&/@OptionValue["ReactionStyle"]);
 	corners=getCorners[rxnPos];
 	aspectRatio=getAspectRatio[Sequence@@corners];
+
 	cleanRxnData=FilterRules[OptionValue["ReactionData"]/.elem_v:>getID[elem],rxnPos[[All,1]]];
+	If[OptionValue["MinMaxHack"]===True,
+		refMax=Max[Abs[{Min[#],Max[#]}&[cleanRxnData[[All,2]]]]];
+		cleanRxnData=Join[cleanRxnData,{"Max"->refMax,"Moritz"->-refMax}];
+	];
+	If[MatchQ[OptionValue["MinMaxHack"],{_?NumberQ,_?NumberQ}],
+		{refMin,refMax}=OptionValue["MinMaxHack"];
+		cleanRxnData=Join[cleanRxnData,{"Max"->refMin,"Moritz"->refMax}];
+	];
+
+	scalingFunction=Switch[OptionValue["ColorFunctionScaling"],True,If[directedQ,Rescale[Abs@#,{Min[Abs@#],Max[Abs@#]},{0.,1.}]&,Rescale[#,{Min[#],Max[#]},{0.,1.}]&],_Function,OptionValue["ColorFunctionScaling"],False,#&];
 	cleanMetaboliteData=FilterRules[OptionValue["MetaboliteData"]/.elem:$MASS$speciesPattern:>getID[elem],metPos[[All,1]]];
-	fluxStyle=Thread[Rule[cleanRxnData[[All,1]]/.elem_v:>getID[elem],Thread[List[Arrowheads/@Rescale[Abs@#,{Min[Abs@#],Max[Abs@#]},{OptionValue["MinThickness"]*5,OptionValue["MaxThickness"]*5}],Thickness/@Rescale[Abs@#,{Min[Abs@#],Max[Abs@#]},{OptionValue["MinThickness"],OptionValue["MaxThickness"]}],OptionValue["ColorFunction"]/@scalingFunction[#],-1*Sign[#]]]]]&[cleanRxnData[[All,2]]];
+	If[directedQ,
+		fluxStyle=Thread[Rule[cleanRxnData[[All,1]]/.elem_v:>getID[elem],Thread[List[Arrowheads/@Rescale[Abs@#,{Min[Abs@#],Max[Abs@#]},{OptionValue["MinThickness"]*(5/aspectRatio),OptionValue["MaxThickness"]*(5/aspectRatio)}],Thickness/@Rescale[Abs@#,{Min[Abs@#],Max[Abs@#]},{OptionValue["MinThickness"],OptionValue["MaxThickness"]}],OptionValue["ColorFunction"]/@scalingFunction[#],-1*Sign[#]]]]]&[cleanRxnData[[All,2]]];,
+		fluxStyle=Thread[Rule[cleanRxnData[[All,1]]/.elem_v:>getID[elem],Thread[List[Thickness/@Rescale[Abs@#,{Min[Abs@#],Max[Abs@#]},{OptionValue["MinThickness"],OptionValue["MaxThickness"]}],OptionValue["ColorFunction"]/@scalingFunction[#],-1*Sign[#]]]]]&[cleanRxnData[[All,2]]];
+	];
+
 	metStyle=Thread[Rule[cleanMetaboliteData[[All,1]],Thread[List[PointSize/@Rescale[#,{Min[#],Max[#]},{OptionValue["MinSize"],OptionValue["MaxSize"]}],OptionValue["ColorFunction"]/@scalingFunction[#](*Rescale[#,{Min[#],Max[#]},{0.,1.}]*)]]]]&[cleanMetaboliteData[[All,2]]];
 	If[OptionValue["Boundary"],
 		cellMembrane=Graphics[{Opacity[0.],EdgeForm[{Thin,Black}],Scale[#,.99]&@Rectangle[Sequence@@Partition[corners[[{1,3,2,4}]],2],RoundingRadius->Scaled[.1]]}];,
@@ -440,7 +469,10 @@
 		drawMetaboliteMap[metPos,Sequence@@updateRules[OptionValue["MetaboliteStyle"],If[metStyle=!={},{"Style"->metStyle},{}]],Sequence@@FilterRules[{opts},Options[drawMetaboliteMap]]],Graphics@Style[textPos,Sequence@@(OptionValue["TextStyle"]/.elem:(_Scaled):>elem[[0]][elem[[1]]*(1/aspectRatio)])],
 		ImageSize->OptionValue["ImageSize"]
 	];
-	map=If[OptionValue["PlotLegends"]=!=None&&OptionValue["ReactionData"]=!={},Legended[map,BarLegend[{OptionValue["ColorFunction"][[1]],{0,Max@Abs@cleanRxnData[[All,2]]}},If[MatchQ[OptionValue["PlotLegends"],{_Rule..}],Sequence@@OptionValue["PlotLegends"],Unevaluated[Sequence[]]]]],map];
+	map=If[OptionValue["PlotLegends"]=!=None&&OptionValue["ReactionData"]=!={},
+		{min,max}={If[directedQ,0,Min[#]],If[directedQ,Max@Abs@#,Max@#]}&[cleanRxnData[[All,2]]];
+		helperFunc=Composition[#,With[{minn=min,maxx=max},Rescale[#,{minn,maxx},{0.,1.}]&]]&;
+		Legended[map,BarLegend[{If[MatchQ[OptionValue["ColorFunction"],_ColorDataFunction],OptionValue["ColorFunction"][[1]],helperFunc[OptionValue["ColorFunction"]][#]&],{min,max}},If[MatchQ[OptionValue["PlotLegends"],{_Rule..}],Sequence@@OptionValue["PlotLegends"],Unevaluated[Sequence[]]]]],map];
 	map
 ];
 def:drawPathway[___]:=(Message[Toolbox::badargs,drawPathway,Defer@def];Abort[])
@@ -477,7 +509,7 @@
 
 Unprotect[drawNodeMaps];
 Options[drawNodeMaps]={"Fluxes"->{},"Metabolites"->{},ColorFunction->ColorData["Rainbow"],"Legend"->False};
-drawNodeMaps[model_MASSmodel,opts:OptionsPattern[{drawNodeMaps,GraphPlot}]]:=Module[{stoichRules,minFlux,maxFlux,colorFunction,activeFluxes,directions,bip,activeBip,nodeMapGraphs,edgeThicknesses,colorValues,edgeRenderingFunc,nodeRenderingFunc,metabolites,legendFunc,netFluxes},
+drawNodeMaps[model_MASSmodel,opts:OptionsPattern[{drawNodeMaps,GraphPlot}]]:=Module[{unitlessFluxes,stoichRules,minFlux,maxFlux,colorFunction,activeFluxes,directions,bip,activeBip,nodeMapGraphs,edgeThicknesses,colorValues,edgeRenderingFunc,nodeRenderingFunc,metabolites,legendFunc,netFluxes},
 	stoichRules={model["Species"][[#[[1,1]]]],model["Fluxes"][[#[[1,2]]]]}->Abs[#[[2]]]&/@ArrayRules[model["SparseStoichiometry"]][[;;-2]];
 	colorFunction=If[OptionValue["Fluxes"]==={},Black&,OptionValue["ColorFunction"]];
 	netFluxes=Thread[model["Species"]->model.model["Fluxes"]];