Description of RxnAdjuster

0001 function [OverlayMe,Allx4Arrow,Ally4Arrow] = RxnAdjuster(PostData,Mdl,RefID)
0002 % RxnAdjuster
0003 % is a subfunction of MapAdjuster for displaying reaction
0004 % details on created maps by NetDraw.
0005 %
0006 % Inputs:
0007 % PostData: All necessary data from NetDraw
0008 % Mdl: COBRA model for which in silico simulations are performed.
0009 % RefID: A string; 'bigg' or 'kegg'.
0010 
0011 % O. Jamialahmadi
0012 % TMU, Chem. Eng. Dept., Biotech. Group
0013 % July 2016
0014 
0015 Allx4Arrow = PostData.Allx4Arrow;
0016 Ally4Arrow = PostData.Ally4Arrow;
0017 field_intsect = PostData.field_intsect;
0018 Idxs = PostData.field_intsect_overlay;
0019 rxnCds = PostData.rxnCds;
0020 [~,n2] = ismember(Idxs,field_intsect);
0021 OrxnCds = rxnCds(n2);
0022 ArXo = PostData.ArXo;
0023 ArYo = PostData.ArYo;
0024 RefOverlapData = PostData.RefOverlapData;
0025 [~,Idx1,~] = unique(RefOverlapData);
0026 Chck1 = setdiff(1:size(RefOverlapData,1),Idx1);
0027 
0028 for m2 = 1:numel(Chck1)
0029     WhrC = ismember(RefOverlapData,RefOverlapData{Chck1(m2)});
0030     RedundantIdx = field_intsect(WhrC);
0031     if any(ismember(Idxs,RedundantIdx))
0032         if sum(ismember(Idxs,RedundantIdx)) < numel(RedundantIdx)
0033             Allx4Arrow(WhrC) = {''}; Ally4Arrow(WhrC) = {''}; 
0034             field_intsect(WhrC) = {''};
0035             WhrAdd = find(ismember(Idxs,RedundantIdx));
0036             for m3 = 1:numel(WhrAdd)
0037                 Allx4Arrow{end+1} = ArXo{WhrAdd(m3)};
0038                 Ally4Arrow{end+1} = ArYo{WhrAdd(m3)};
0039                 field_intsect(end+1) = Idxs(WhrAdd(m3));
0040             end
0041         end      
0042     end   
0043 end
0044 emrmv = ~cellfun('isempty',field_intsect);
0045 Allx4Arrow = Allx4Arrow(emrmv);
0046 Ally4Arrow = Ally4Arrow(emrmv);
0047 field_intsect = field_intsect(emrmv); NewRefData = ({});
0048 for i1 =1:numel(Allx4Arrow)
0049     NewRefData{i1} = [num2str(numel(Allx4Arrow{i1})),',',...
0050         num2str(mean(Allx4Arrow{i1})),',',num2str(numel(Ally4Arrow{i1})),',',...
0051         num2str(mean(Ally4Arrow{i1}))];
0052 end
0053 [~,Idx1,~] = unique(NewRefData); clear WhrC
0054 Chck1 = setdiff(1:size(NewRefData,2),Idx1);
0055 [~,N2] = ismember(field_intsect,PostData.field_intsect);
0056 switch RefID
0057     case 'kegg'
0058         OverlayMe = rxnCds(N2);
0059     case 'bigg'
0060         K1 = Mdl.B2Kegg.K;
0061         B1 = Mdl.B2Kegg.B;
0062         Chk = which('UniModelKEGG.mat');
0063         if isempty(Chk)
0064             msgbox({'UniModelKEGG.mat cannot be found!';...
0065                 'Make sure the file is present in BiGG2KEGG folder'},'Error','error');
0066             return
0067         end
0068         CRxns = getappdata(0,'CRxns');
0069         OverlayMe = rxnCds(N2);
0070         if ~isempty(CRxns) % Correct for consistent reaction correspondences
0071             for cnter = 1:numel(CRxns.C)
0072                 OverlayMe(ismember(OverlayMe,CRxns.C{cnter})) = ...
0073                     CRxns.O(cnter);
0074                 OrxnCds(ismember(OrxnCds,CRxns.C{cnter})) = ...
0075                     CRxns.O(cnter);
0076             end
0077         end
0078         
0079         Uni = load(which('UniModelKEGG.mat'));
0080         K = Uni.B2Kegg.K;
0081         B = Uni.B2Kegg.B;
0082         for i1 = 1:numel(OverlayMe)
0083             if any(strcmp(OverlayMe{i1},OrxnCds))
0084                 WhrK = find(ismember(K1,OverlayMe{i1}));
0085                 if isempty(WhrK)
0086                     WhrK = find(ismember(K,OverlayMe{i1}));
0087                     Tmpchk = B(WhrK);
0088                 else
0089                     Tmpchk = B1(WhrK);
0090                 end
0091             else
0092                 WhrK = find(ismember(K,OverlayMe{i1}));
0093                 Tmpchk = B(WhrK);
0094             end
0095             if isempty(WhrK)
0096                 OverlayMe(i1) = {''};
0097                 continue
0098             end
0099             if numel(WhrK)>1                
0100                 C1 = regexp(Tmpchk,'\w*p\>'); C1 = ~cellfun('isempty',C1);
0101                 if sum(C1) < numel(Tmpchk)
0102                     Tmpchk(C1) = [];
0103                 end
0104                 C1 = regexp(Tmpchk,'\w*copy\d\>'); C1 = ~cellfun('isempty',C1);
0105                 if sum(C1) < numel(Tmpchk)
0106                     Tmpchk(C1) = [];
0107                 end
0108                 C1 = regexp(Tmpchk,'\w*f\>'); C1 = ~cellfun('isempty',C1);
0109                 if sum(C1) < numel(Tmpchk)
0110                     Tmpchk(C1) = [];
0111                 end
0112                 C1 = regexp(Tmpchk,'\w*m\>'); C1 = ~cellfun('isempty',C1);
0113                 if sum(C1) < numel(Tmpchk)
0114                     Tmpchk(C1) = [];
0115                 end
0116                 C1 = regexp(Tmpchk,'ICDHhr'); C1 = ~cellfun('isempty',C1);
0117                 if sum(C1) < numel(Tmpchk)
0118                     Tmpchk(C1) = [];
0119                 end
0120             end
0121             OverlayMe(i1) = Tmpchk(1);
0122         end
0123 end
0124 Allx4Arrow = PostData.Allx4Arrow(N2);
0125 Ally4Arrow = PostData.Ally4Arrow(N2);
0126 overlayMetemp = OverlayMe;
0127 for m2 = 1:numel(Chck1)
0128     WhrC = find(ismember(NewRefData,NewRefData{Chck1(m2)}));
0129     for m3 = 1:numel(WhrC)
0130         OverlayMe{WhrC(m3)} = strjoin(overlayMetemp(WhrC),',');
0131         if ~isempty(OverlayMe{WhrC(m3)})       
0132             if strcmp(OverlayMe{WhrC(m3)}(1),',')
0133                 OverlayMe{WhrC(m3)}(1) = [];
0134             end
0135         end
0136         if ~isempty(OverlayMe{WhrC(m3)})
0137             if strcmp(OverlayMe{WhrC(m3)}(end),',')
0138                 OverlayMe{WhrC(m3)}(end) = [];
0139             end
0140         end
0141     end
0142 end
0143 [~,N1] = unique(OverlayMe);
0144 OverlayMe = OverlayMe(N1); Allx4Arrow = Allx4Arrow(N1); Ally4Arrow = Ally4Arrow(N1);
RxnAdjuster

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SOURCE CODE
