diff --git a/createTestData/evaluateProFitFittingParameters.m b/createTestData/evaluateProFitFittingParameters.m
index 663aa23f462b35cb41738f30643b955fdd2142b4..5766a57fa4fc740508ea5a353bd7a6b68ac35ddc 100644
--- a/createTestData/evaluateProFitFittingParameters.m
+++ b/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;
diff --git a/createTestData/plotSimulationResults.m b/createTestData/plotSimulationResults.m
index 34ba99c52f6a0f06f3e9d853ba538fc5856443a0..9dd34134cd823fac21171ef45fbac324a941cd3d 100644
--- a/createTestData/plotSimulationResults.m
+++ b/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;