Worked on how to plot portrait figures. It is complicated. Don't scale the...

Worked on how to plot portrait figures. It is complicated. Don't scale the figure too much in the height to avoid rescaling of text.
Also try stepwise to export it and verify tiff.
Created multiple subplots for the correlation plots in plotSimulationResults

createTestData/evaluateProFitFittingParameters.m

@@ -27,8 +27,10 @@ titleLabels = {'\Delta\varphi_0', '\Delta\varphi_1', '\Delta\nu_g', '${\boldmath
     '${\boldmath$\overline{\mid\Delta\nu_{e}\mid}$}$', '${\boldmath$\overline{\mid\Delta c\mid}$}$', '${\boldmath$\overline{\mid\Delta T_{2}\mid}$}$'};
 units = {          ' (degrees)',     ' (degrees/ppm)', ' (Hz)',         ' (Hz)',...
     ' (Hz)',                                   ' (mmol/kg)',                            ' (ms)'};
-titleOffset = {'\quad variations:\quad\quad','\quad variations:\quad', '\quad variations:\quad\quad\quad', '\quad variations:\quad\quad',...
-    '\quad variations:\quad\quad',     '\quad variations:\quad',        '\quad variations:\quad\quad'};
+% titleOffset = {'\quad variations:\quad\quad','\quad variations:\quad', '\quad variations:\quad\quad\quad', '\quad variations:\quad\quad',...
+%     '\quad variations:\quad\quad',     '\quad variations:\quad',        '\quad variations:\quad\quad'};
+titleOffset = {'\quad variations:\quad','\quad variations:\,\,', '\quad variations:\quad\quad', '\quad variations:\quad',...
+    '\quad variations:\quad',     '\quad variations:\,\,',        '\quad variations:\quad'};
 % parameters = {'conc'};
 
 useSubPlots =  true;

createTestData/plotSimulationResults.m

@@ -303,6 +303,7 @@ end
 xlswrite([dataExportPathBase, 'SimulationsTable2.xlsx'],metaboliteTable);
 end
 
+%% get metabolite concentrations for a given paramKeyword and create the requested plots
 function [allSimulMetConc, allLCModelMetConc, allProFitMetConc, allLCModelMetConcDev, allProFitMetConcDev, metaboliteTable, figIds, figIdsCorr,...
     allMeanProFit, allStdProFit,allMeanProFitMain, allStdProFitMain] = ...
     getConcentrations(metabolites, metabolitesLCModel, metabolitesProFit, metabolitesToDisplay, metabolitesLabels, ...
@@ -355,6 +356,7 @@ metaboliteTable{numberOfMet+4,indexTable}   = [num2str(allMeanProFitMain,'%.1f')
 metaboliteTable{numberOfMet+4,indexTable+1} = [num2str(allMeanLCModelMain,'%.1f'),  plusMinusSign, num2str(allStdLCModelMain,'%.1f')];
 end
 
+%% reorganize the fitted concentrations to 2D tables
 function [allSimulMetConc, allLCModelMetConc, allProFitMetConc, allLCModelMetConcDev, allProFitMetConcDev] = ...
     reorganizeMetConcentrationsToMatrices(metabolites, metabolitesLCModel, metabolitesProFit, ...
     concentrationsRm, concentrationsLCModel, concentrationsProFit, activeMetabolites, scalingOn)
@@ -407,6 +409,7 @@ for indexMetabolite = 1:numberOfMet
 end
 end
 
+%% plot Correlation plots between the fitted ProFit, LCModel concentrations and the true simulated concentrations
 function figIdsCorr = plotCorrelationFigs(concentrationsRm, allLCModelMetConc, allProFitMetConc,...
     metabolitesToDisplay, numberOfMet, dataExportPathBase, paramKeyword, truncSuffix, figIdsCorr)
 
@@ -416,40 +419,107 @@ if isempty(figIdsCorr)
 else
     emptyFigureIdsCorr = false;
 end
+
+% Main Figure = 12 subplots
+figureMainRows = 4;
+figureMainCols = 3;
+metabolitesFigureMain = {'NAA(CH_2)', 'tCho+', 'mI', 'sI','Gly','Glu','Gln',...
+    'GABA', 'Lac', 'GSH', 'NAAG', 'MM spectrum'};
+figID_Main = figure();
+mainFigureRunningIndex = 0;
+% Supporting Figure = 5 subplots
+figureSupportingRows = 3;
+figureSupportingCols = 4;
+metabolitesFigureSupporting = {'tCr(CH_3)', 'tCr(CH_2)', 'NAA(CH_3)','Asp','Tau'};
+figID_Supporting = figure();
+supportingFigureRunningIndex = 0;
+
+colorOriginal = [0 0 0];
+colorProFit = [0.49 0.18 0.56];
+colorLCModel = [0.85 0.33 0.1];
+
 for indexMetabolite = 1:numberOfMet  
     simulatedMetConc     = concentrationsRm(:, indexMetabolite);
     fittedMetConcLCModel = allLCModelMetConc(:, indexMetabolite);
     fittedMetConcProFit  = allProFitMetConc(:, indexMetabolite);
-    if emptyFigureIdsCorr
-        figIdsCorr{indexMetabolite} = figure;
+%     if emptyFigureIdsCorr
+%         figIdsCorr{indexMetabolite} = figure;
+%     end
+%     figure(figIdsCorr{indexMetabolite});
+    if sum(contains(metabolitesFigureMain, metabolitesToDisplay{indexMetabolite}))
+        figure(figID_Main);
+        mainFigureRunningIndex = mainFigureRunningIndex + 1;
+        subplot(figureMainRows, figureMainCols, mainFigureRunningIndex);
+        if mod(mainFigureRunningIndex,figureMainCols)== 1
+            plotYLabel = true;
+        else
+            plotYLabel = false;
+        end
+        if round((mainFigureRunningIndex+1)/figureMainCols)== figureMainRows
+            plotXLabel = true;
+        else
+            plotXLabel = false;
+        end
+    elseif sum(contains(metabolitesFigureSupporting, metabolitesToDisplay{indexMetabolite}))
+        figure(figID_Supporting);
+        supportingFigureRunningIndex = supportingFigureRunningIndex + 2;
+        if round((supportingFigureRunningIndex+1)/figureSupportingCols)== figureSupportingRows % offset plot
+            supportingFigureRunningIndex = supportingFigureRunningIndex + 1;
+        end
+        subplot(figureSupportingRows, figureSupportingCols, supportingFigureRunningIndex-1:supportingFigureRunningIndex)
+        if mod(supportingFigureRunningIndex-1,figureSupportingCols)<= 2
+            plotYLabel = true;
+        else
+            plotYLabel = false;
+        end
+        if round((supportingFigureRunningIndex+1)/figureSupportingCols)>= figureSupportingRows-1
+            plotXLabel = true;
+        else
+            plotXLabel = false;
+        end
+    else
+        warning('Metabolite not associated with either main or supporting figure: ', metabolitesToDisplay{indexMetabolite});
+        figure();
+        plotYLabel = true;
+        plotXLabel = true;
+    end
+    
+    if strcmp(metabolitesToDisplay(indexMetabolite),'MM spectrum')
+        simulatedMetConc     = simulatedMetConc *1e-7;
+        fittedMetConcLCModel = fittedMetConcLCModel *1e-7;
+        fittedMetConcProFit  = fittedMetConcProFit *1e-7;
     end
-    figure(figIdsCorr{indexMetabolite});
     hold on
-    scatter(simulatedMetConc, fittedMetConcLCModel);
-    scatter(simulatedMetConc, fittedMetConcProFit, 'x');
-    plot(simulatedMetConc,simulatedMetConc);
+    scatter(simulatedMetConc, fittedMetConcLCModel, 'MarkerEdgeColor', colorLCModel);
+    scatter(simulatedMetConc, fittedMetConcProFit, 'x', 'MarkerEdgeColor', colorProFit);
+    offSetEnds = max(simulatedMetConc)*0.05;
+    identityLine = min(simulatedMetConc)-offSetEnds:0.01:max(simulatedMetConc)+offSetEnds;
+    plot(identityLine,identityLine,'color',colorOriginal);
     title(metabolitesToDisplay(indexMetabolite))
     
-    xlabel('Simulated concentrations {\boldmath$c$}$_{k}$ (mmol/kg)', 'Interpreter', 'latex')
-    ylabel('Fitted concentrations {\boldmath$c$}$_{k}$ (mmol/kg)', 'Interpreter', 'latex')
-    legend('LCModel {\boldmath$c$}$_{k}$', 'ProFit {\boldmath$c$}$_{k}$', 'Identity Line', 'Location', 'Northwest', 'Interpreter', 'latex')
-    set(gca, 'FontSize', 13)
-    xl = xlim;
-    if xl(2) > max(simulatedMetConc)
-        xl(2) = max(simulatedMetConc);
+    if plotXLabel
+        xlabel('$c_{k}^{simulated} \,\, (mmol/kg)$', 'Interpreter', 'latex')
     end
-    xlim(xl);
-    
-    pathName = [dataExportPathBase, paramKeyword, '/correlations/'];
-    if ~exist(pathName, 'dir')
-        mkdir(pathName);
+    if plotYLabel
+        ylabel('$c_k^{fitted} \,\, (mmol/kg)$', 'Interpreter', 'latex')
     end
-    fileName = [metabolitesToDisplay{indexMetabolite}, '_', paramKeyword, truncSuffix];
-    saveas(figIdsCorr{indexMetabolite}, [pathName, fileName, '.tif']);
-    savefig(figIdsCorr{indexMetabolite}, [pathName,fileName, '.fig'],'compact');
+    legend('$LCModel \,\, c_k^{fitted}$', '$ProFit \,\, c_k^{fitted}$', '$Identity \, Line$', 'Location', 'best', 'Interpreter', 'latex')
+    set(gca, 'FontSize', 13)
+
+    xlim([min(identityLine),max(identityLine)])
+    ylim([min(identityLine),max(identityLine)])
+    
+%     pathName = [dataExportPathBase, paramKeyword, '/correlations/'];
+%     if ~exist(pathName, 'dir')
+%         mkdir(pathName);
+%     end
+%     fileName = [metabolitesToDisplay{indexMetabolite}, '_', paramKeyword, truncSuffix];
+%     saveas(figIdsCorr{indexMetabolite}, [pathName, fileName, '.tif']);
+%     savefig(figIdsCorr{indexMetabolite}, [pathName,fileName, '.fig'],'compact');
 end
 end
 
+%% plot Precision plots with boxplots showing percentages
 function figIds = plotPrecisionFigs(figIds, numberOfMet, offsetPlot, secondaryFigures, plotColors, ...
     allLCModelMetConcDev, allProFitMetConcDev, metabolitesLabels)
 
@@ -498,6 +568,7 @@ function figIds = plotPrecisionFigs(figIds, numberOfMet, offsetPlot, secondaryFi
     yline(0,':', 'Color',[0.5 0.5 0.5]);
 end
 
+%% setup the table to show metabolite concentration changes
 function [metaboliteTable, indexTable] = setupTable(numberOfMet, numOfParameters, metabolitesLabels)
 metaboliteTable = cell(numberOfMet+4,numOfParameters*2+1);
 metaboliteTable(3:numberOfMet+2,1) = metabolitesLabels;