colorSubsystem

 Modified from colorSubsystemCD as distributed through COBRA Toolbox
 https://github.com/opencobra/cobratoolbox/blob/src/visualization/metabolicCartography/colorSubsystemCD.m

 Color every reaction in a specific subsystem

 USAGE:

   [newMap] = colorSubsystemCD(map, model, subsystem, color, areaWidth);

 INPUTS:
   map:            File from CellDesigner parsed to MATLAB format
   model:          COBRA model structure
   subsystem:      Name of a subsystem as a String

 OPTIONAL INPUTS:
   color:          Color desired for reactions in CAPITALS
   areaWidth:          Width desired for reactions

 OUTPUT:
   newMap          MATLAB structure of map with reaction modifications

0001 function newMap = colorSubsystem(map, model, subsystem, color)
0002 % Modified from colorSubsystemCD as distributed through COBRA Toolbox
0003 % https://github.com/opencobra/cobratoolbox/blob/src/visualization/metabolicCartography/colorSubsystemCD.m
0004 %
0005 % Color every reaction in a specific subsystem
0006 %
0007 % USAGE:
0008 %
0009 %   [newMap] = colorSubsystemCD(map, model, subsystem, color, areaWidth);
0010 %
0011 % INPUTS:
0012 %   map:            File from CellDesigner parsed to MATLAB format
0013 %   model:          COBRA model structure
0014 %   subsystem:      Name of a subsystem as a String
0015 %
0016 % OPTIONAL INPUTS:
0017 %   color:          Color desired for reactions in CAPITALS
0018 %   areaWidth:          Width desired for reactions
0019 %
0020 % OUTPUT:
0021 %   newMap          MATLAB structure of map with reaction modifications
0022 if nargin < 4
0023     color = 'RED';
0024 end
0025 
0026 newMap = map;
0027 rxnList = model.rxns(ismember([model.subSystems{:}]', subsystem));
0028 colors = createColorsMap;
0029 
0030 index = find(ismember(newMap.rxnName, rxnList));
0031 for j = index'
0032     newMap.rxnColor{j, 1} = colors(color);
0033     %newMap.rxnWidth{j, 1} = areaWidth;
0034 end
0035 
0036 % Use the existence of reactant lines to check if the map has the
0037 % complete structure, and if so change also secondary lines.
0038 if any(strcmp('rxnReactantLineColor', fieldnames(newMap))) == 1
0039     for j = index'
0040         if ~isempty(newMap.rxnReactantLineColor{j})
0041             for k = 1:length(newMap.rxnReactantLineColor{j})
0042                 newMap.rxnReactantLineColor{j, 1}{k, 1} = colors(color);
0043                 %newMap.rxnReactantLineWidth{j, 1}{k, 1} = areaWidth;
0044             end
0045         end
0046         if ~isempty(newMap.rxnProductLineColor{j})
0047             for m = 1:1:length(newMap.rxnProductLineColor{j})
0048                 newMap.rxnProductLineColor{j, 1}{m, 1} = colors(color);
0049                 %newMap.rxnProductLineWidth{j, 1}{m, 1} = areaWidth;
0050             end
0051         end
0052     end
0053 end
0054 
0055 end