flx2col

 flx2col
 Performs color mapping for caculated flux values and normalizes them based on
 maximum and minimum flux values in the input data.
 This function uses following inputs:
 1- BoxCol: RGB code entered by user for background color of each box
 2- flx : Contains flux values in form of:
       2-1 A 2D matrix, in which each column represents flux values for
           each state of one certain species/model (i.e. dynamic state 
           of a certain model extracted from COBRA Toolbox). In this
           situation flx may contain various columns, indicating different
           circumstances of a certain species.
       2-2 A 2D matrix, in which each column represents flux valuse for
           each state of two different species/models (similarly, from
           COBRA Toolbox). In this situation, if a dynamic comparison
           between two species/models is performed, the number of flx
           columns must be even. 
       2-3 A column vector. This situation is similar to case 1-1, but in
           static state.
 3- Cm : A colormap based on MATLAB built-in colormaps.
 4- I : The output of imread, containing RGB values of KEGG map pixels.
 5- k, m : Column and row indices, respectively.
 6- idx : Coordinates of each enzyme box on a KEGG map image, extracted
          from corresponding KGML file
 7- idw : Width of each box corresponding to idx, extracted from KGML
          file
 8- Tempx : Indicates the height of each box which should be colored
 9- Thresh: Threshold for each flux value, which lower than this threshold
            the box will be left blank, suggesting that the flx value is
            near zero.

0001 function I = flx2col(BoxCol,flx,Cm,I,k,flxMax,flxMin,m,idx,idw,Tempx,Thresh)
0002 % flx2col
0003 % Performs color mapping for caculated flux values and normalizes them based on
0004 % maximum and minimum flux values in the input data.
0005 % This function uses following inputs:
0006 % 1- BoxCol: RGB code entered by user for background color of each box
0007 % 2- flx : Contains flux values in form of:
0008 %       2-1 A 2D matrix, in which each column represents flux values for
0009 %           each state of one certain species/model (i.e. dynamic state
0010 %           of a certain model extracted from COBRA Toolbox). In this
0011 %           situation flx may contain various columns, indicating different
0012 %           circumstances of a certain species.
0013 %       2-2 A 2D matrix, in which each column represents flux valuse for
0014 %           each state of two different species/models (similarly, from
0015 %           COBRA Toolbox). In this situation, if a dynamic comparison
0016 %           between two species/models is performed, the number of flx
0017 %           columns must be even.
0018 %       2-3 A column vector. This situation is similar to case 1-1, but in
0019 %           static state.
0020 % 3- Cm : A colormap based on MATLAB built-in colormaps.
0021 % 4- I : The output of imread, containing RGB values of KEGG map pixels.
0022 % 5- k, m : Column and row indices, respectively.
0023 % 6- idx : Coordinates of each enzyme box on a KEGG map image, extracted
0024 %          from corresponding KGML file
0025 % 7- idw : Width of each box corresponding to idx, extracted from KGML
0026 %          file
0027 % 8- Tempx : Indicates the height of each box which should be colored
0028 % 9- Thresh: Threshold for each flux value, which lower than this threshold
0029 %            the box will be left blank, suggesting that the flx value is
0030 %            near zero.
0031 
0032 % O. Jamialahmadi
0033 % TMU, Chem. Eng. Dept., Biotech. Group
0034 % Feb. 2015
0035 % Modified: Lines 70-78 for zero carrying fluxes
0036 % =========================================================================
0037 
0038 % Normalization of color indices in Cm, Red for highest flux and
0039 % Blue for lowest flux.
0040 flx = abs(flx);
0041 % flxMax=max(abs(flx(:,k)));
0042 % flxMin=min(abs(flx(:,k)));
0043 % if flxMax==flxMin % One row (i.e. for 1 rxn)
0044 %     flxMax=max(abs(flx(m,:)));
0045 %     flxMin=min(abs(flx(m,:)));
0046 % end
0047     flxSl=(size(Cm,1)-1)./(flxMax-flxMin);
0048     if isinf(flxSl) % in case of flxMax == flxMin
0049         flxSl = 1e15.*(size(Cm,1)-1);
0050     end
0051     Mcm=ceil((flx(m,k)-flxMax).*flxSl+size(Cm,1));
0052     Tempy=(round(idx(m)+1):round(idx(m)+idw(m)-1));
0053 if flxMax > 0   
0054     [x1,y1]=find(I(Tempx,Tempy,1)==0 & I(Tempx,Tempy,2)==0 & I(Tempx,Tempy,3)==0);
0055     Tempy1=round(idx(m)+1):round(idx(m)+(flx(m,k)*idw(m))./flxMax-1);
0056     Tempy2=round(idx(m)+(flx(m,k)*idw(m))./flxMax)-1:(idx(m)+idw(m)-1);
0057     [x2,y2]=find(I(Tempx,Tempy1,1)==0 & I(Tempx,Tempy1,2)==0 & I(Tempx,Tempy1,3)==0);
0058     I(Tempx,Tempy1,1)=Cm(Mcm,1);
0059     I(Tempx,Tempy1,2)=Cm(Mcm,2);
0060     I(Tempx,Tempy1,3)=Cm(Mcm,3);
0061     if isempty(BoxCol) % Default color
0062         I(Tempx,Tempy2,1)=169;%Dark gray for background of each box
0063         I(Tempx,Tempy2,2)=169;
0064         I(Tempx,Tempy2,3)=169;
0065     else % User defined color
0066         I(Tempx,Tempy2,1)=BoxCol(1);
0067         I(Tempx,Tempy2,2)=BoxCol(2);
0068         I(Tempx,Tempy2,3)=BoxCol(3);
0069     end
0070 end
0071 if abs(flx(m,k))< Thresh % Threshold for considering a flux = 0
0072     if isempty(BoxCol) % Default color
0073         for g1=1:length(x1)
0074             I(Tempx(x1(g1)),Tempy(y1(g1)),:)=169;
0075         end
0076     else
0077         I(Tempx,Tempy,1)=BoxCol(1);
0078         I(Tempx,Tempy,2)=BoxCol(2);
0079         I(Tempx,Tempy,3)=BoxCol(3);
0080     end
0081 else
0082     for g1=1:length(x2)
0083         I(Tempx(x2(g1)),Tempy1(y2(g1)),1)=Cm(Mcm,1);
0084         I(Tempx(x2(g1)),Tempy1(y2(g1)),2)=Cm(Mcm,2);
0085         I(Tempx(x2(g1)),Tempy1(y2(g1)),3)=Cm(Mcm,3);
0086     end
0087 end
0088 end