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Commit 8137b895 authored by Tamas Borbath's avatar Tamas Borbath
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Just restructured the code of plotSimulationResults.m to allow better modifications.

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createTestData/plotSimulationResults.m
+ 188
− 165
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...@@ -142,7 +142,7 @@ xOffset = 0.65; ...@@ -142,7 +142,7 @@ xOffset = 0.65;
yOffsetRect = 0.085; %0.075; -for two subfigures yOffsetRect = 0.085; %0.075; -for two subfigures
for indexSim = 1:4 for indexSim = 1:4
yOffset = 0.84;% 4 subfigs%0.80; - Two figs placed lower%0.86 -Two figs yOffset = 0.84;% 4 subfigs%0.80; - Two figs placed lower%0.86 -Two figs
annotation('textbox',[xOffset yOffset 0.1 0.1],'String',str{indexSim},'FitBoxToText','On', ... annotation('textbox',[xOffset yOffset 0.1 0.1],'String',str{indexSim},'FitBoxToText','On', ...
'EdgeColor','none', 'FontSize', 12, 'Interpreter','latex','Color',plotColors{indexSim}) 'EdgeColor','none', 'FontSize', 12, 'Interpreter','latex','Color',plotColors{indexSim})
annotation('rectangle',[xOffset-0.012 yOffset+yOffsetRect 0.01 0.01],'EdgeColor','none', 'FaceColor',plotColors{indexSim}) annotation('rectangle',[xOffset-0.012 yOffset+yOffsetRect 0.01 0.01],'EdgeColor','none', 'FaceColor',plotColors{indexSim})
yOffset = 0.612;% 4 subfigs%0.37; - Two figs placed lower%0.37 -Two figs yOffset = 0.612;% 4 subfigs%0.37; - Two figs placed lower%0.37 -Two figs
...@@ -153,7 +153,7 @@ for indexSim = 1:4 ...@@ -153,7 +153,7 @@ for indexSim = 1:4
end end
% save Table % save Table
xlswrite([dataExportPathBase, 'SimulationsTable1.xlsx'],metaboliteTable); xlswrite([dataExportPathBase, 'SimulationsTable1.xlsx'],metaboliteTable);
numOfParameters2 = 5; numOfParameters2 = 5;
[metaboliteTable, indexTable] = setupTable(numberOfMet, numOfParameters2, metabolitesLabels); [metaboliteTable, indexTable] = setupTable(numberOfMet, numOfParameters2, metabolitesLabels);
...@@ -260,7 +260,7 @@ concentrationsLCModel = concentrations; ...@@ -260,7 +260,7 @@ concentrationsLCModel = concentrations;
load([dataExportPathBase, 'concentrations_', paramKeyword, truncSuffix, '_profit.mat'], 'concentrations', 'activeMetabolites'); load([dataExportPathBase, 'concentrations_', paramKeyword, truncSuffix, '_profit.mat'], 'concentrations', 'activeMetabolites');
concentrationsProFit = concentrations; concentrationsProFit = concentrations;
plotCorrelations = false; plotCorrelations = true;
offsetPlot = 0.; offsetPlot = 0.;
plotPrecision = false; plotPrecision = false;
indexTable = indexTable +2; indexTable = indexTable +2;
...@@ -290,7 +290,7 @@ xOffset = 0.63; ...@@ -290,7 +290,7 @@ xOffset = 0.63;
yOffsetRect = 0.085; %0.075; -for two subfigures yOffsetRect = 0.085; %0.075; -for two subfigures
for indexSim = 1:4 for indexSim = 1:4
yOffset = 0.392;% 4 subfigs%0.80; - Two figs placed lower%0.86 -Two figs yOffset = 0.392;% 4 subfigs%0.80; - Two figs placed lower%0.86 -Two figs
annotation('textbox',[xOffset yOffset 0.1 0.1],'String',str{indexSim},'FitBoxToText','On', ... annotation('textbox',[xOffset yOffset 0.1 0.1],'String',str{indexSim},'FitBoxToText','On', ...
'EdgeColor','none', 'FontSize', 12, 'Interpreter','latex','Color',plotColors{indexSim}) 'EdgeColor','none', 'FontSize', 12, 'Interpreter','latex','Color',plotColors{indexSim})
annotation('rectangle',[xOffset-0.012 yOffset+yOffsetRect 0.01 0.01],'EdgeColor','none', 'FaceColor',plotColors{indexSim}) annotation('rectangle',[xOffset-0.012 yOffset+yOffsetRect 0.01 0.01],'EdgeColor','none', 'FaceColor',plotColors{indexSim})
yOffset = 0.172;% 4 subfigs%0.37; - Two figs placed lower%0.37 -Two figs yOffset = 0.172;% 4 subfigs%0.37; - Two figs placed lower%0.37 -Two figs
...@@ -300,179 +300,202 @@ for indexSim = 1:4 ...@@ -300,179 +300,202 @@ for indexSim = 1:4
xOffset = xOffset + 0.004*stringLenghts{indexSim}; xOffset = xOffset + 0.004*stringLenghts{indexSim};
end end
xlswrite([dataExportPathBase, 'SimulationsTable2.xlsx'],metaboliteTable); xlswrite([dataExportPathBase, 'SimulationsTable2.xlsx'],metaboliteTable);
end end
function [allSimulMetConc, allLCModelMetConc, allProFitMetConc, allLCModelMetConcDev, allProFitMetConcDev, metaboliteTable, figIds, figIdsCorr,... function [allSimulMetConc, allLCModelMetConc, allProFitMetConc, allLCModelMetConcDev, allProFitMetConcDev, metaboliteTable, figIds, figIdsCorr,...
allMeanProFit, allStdProFit,allMeanProFitMain, allStdProFitMain] = ... allMeanProFit, allStdProFit,allMeanProFitMain, allStdProFitMain] = ...
getConcentrations(metabolites, metabolitesLCModel, metabolitesProFit, metabolitesToDisplay, metabolitesLabels, ... getConcentrations(metabolites, metabolitesLCModel, metabolitesProFit, metabolitesToDisplay, metabolitesLabels, ...
concentrationsRm, concentrationsLCModel, concentrationsProFit, activeMetabolites, ... concentrationsRm, concentrationsLCModel, concentrationsProFit, activeMetabolites, ...
scalingOn, plotCorrelations, dataExportPathBase, paramKeyword, truncSuffix, ... scalingOn, plotCorrelations, dataExportPathBase, paramKeyword, truncSuffix, ...
plotPrecision, plotColors, offsetPlot, figIds, figIdsCorr, metaboliteTable, indexTable, indexesMainMet, secondaryFigures) plotPrecision, plotColors, offsetPlot, figIds, figIdsCorr, metaboliteTable, indexTable, indexesMainMet, secondaryFigures)
numberOfMet = length(metabolites); numberOfMet = length(metabolites);
iterationProFit = 4;
if isempty(figIdsCorr) [allSimulMetConc, allLCModelMetConc, allProFitMetConc, allLCModelMetConcDev, allProFitMetConcDev] = ...
emptyFigureIdsCorr = true; reorganizeMetConcentrationsToMatrices(metabolites, metabolitesLCModel, metabolitesProFit, ...
figIdsCorr = cell(1,numberOfMet); concentrationsRm, concentrationsLCModel, concentrationsProFit, activeMetabolites, scalingOn);
else if plotCorrelations
emptyFigureIdsCorr = false; figIdsCorr = plotCorrelationFigs(concentrationsRm, allLCModelMetConc, allProFitMetConc, metabolitesToDisplay, numberOfMet, ...
end dataExportPathBase, paramKeyword, truncSuffix, figIdsCorr);
allSimulMetConc = concentrationsRm; end
allLCModelMetConc = zeros(size(allSimulMetConc)); if plotPrecision
allProFitMetConc = zeros(size(allSimulMetConc)); figIds = plotPrecisionFigs(figIds, numberOfMet, offsetPlot, secondaryFigures, plotColors, ...
allLCModelMetConcDev = zeros(size(allSimulMetConc)); allLCModelMetConcDev, allProFitMetConcDev, metabolitesLabels);
allProFitMetConcDev = zeros(size(allSimulMetConc)); end
for indexMetabolite = 1:numberOfMet
simulatedMetConc = concentrationsRm(:, indexMetabolite); display([paramKeyword, ' NANs:', num2str(sum(isnan(allLCModelMetConcDev)))]);
indexMetSim = find(strcmp(metabolites,'tCr(CH3)')); %'MMB' meanConcDevLCModel = mean(allLCModelMetConcDev,'omitnan');
fittedMetConcLCModel = zeros(size(simulatedMetConc)); stdConcDevLCModel = std(allLCModelMetConcDev,'omitnan');
for indexFit = 1:length(concentrationsLCModel) display([paramKeyword, ' NANs ProFit:', num2str(sum(isnan(allProFitMetConcDev)))]);
currentConcentrationsLCModel = concentrationsLCModel{indexFit}; meanConcDevProFit = mean(allProFitMetConcDev,'omitnan');
indexMetLCModel = find(strcmp(currentConcentrationsLCModel(1,:),'Cr')); %'Leu' stdConcDevProFit = std(allProFitMetConcDev,'omitnan');
RefConc = currentConcentrationsLCModel{2,indexMetLCModel};
RefConcSim = concentrationsRm(indexFit,indexMetSim); allMeanLCModel = mean(abs(meanConcDevLCModel));
if scalingOn allStdLCModel = mean(abs(stdConcDevLCModel));
scaling = RefConcSim/RefConc; allMeanProFit = mean(abs(meanConcDevProFit));
else allStdProFit = mean(abs(stdConcDevProFit));
scaling = 1;
end allMeanLCModelMain = mean(abs(meanConcDevLCModel(indexesMainMet)));
indexMetLCModel = find(strcmp(currentConcentrationsLCModel(1,:),metabolitesLCModel(indexMetabolite))); allStdLCModelMain = mean(abs(stdConcDevLCModel(indexesMainMet)));
fittedMetConcLCModel(indexFit) = currentConcentrationsLCModel{2,indexMetLCModel}*scaling; allMeanProFitMain = mean(abs(meanConcDevProFit(indexesMainMet)));
end allStdProFitMain = mean(abs(stdConcDevProFit(indexesMainMet)));
fittedMetConcProFit = zeros(size(simulatedMetConc));
for indexFit = 1:length(concentrationsProFit) plusMinusSign = char(177);
currentConcentrationsProFit = concentrationsProFit{indexFit}{iterationProFit}; metaboliteTable{2,indexTable} = 'ProFit';
indexMetProFit = find(strcmp(activeMetabolites{iterationProFit},'Cr')); %'Leu' metaboliteTable{2,indexTable+1} = 'LCModel';
RefConc = currentConcentrationsProFit(indexMetProFit); for indexMet = 1:numberOfMet
RefConcSim = concentrationsRm(indexFit,indexMetSim); metaboliteTable{indexMet+2,indexTable} = [num2str(meanConcDevProFit(indexMet),'%.1f'), plusMinusSign, num2str(stdConcDevProFit(indexMet),'%.1f')];
if scalingOn metaboliteTable{indexMet+2,indexTable+1} = [num2str(meanConcDevLCModel(indexMet),'%.1f'), plusMinusSign, num2str(stdConcDevLCModel(indexMet),'%.1f')];
scaling = RefConcSim/RefConc; end
else
scaling = 1; metaboliteTable{numberOfMet+3,indexTable} = [num2str(allMeanProFit,'%.1f'), plusMinusSign, num2str(allStdProFit,'%.1f')];
end metaboliteTable{numberOfMet+3,indexTable+1} = [num2str(allMeanLCModel,'%.1f'), plusMinusSign, num2str(allStdLCModel,'%.1f')];
indexMetProFit = find(strcmp(activeMetabolites{iterationProFit},metabolitesProFit(indexMetabolite)));
fittedMetConcProFit(indexFit) = currentConcentrationsProFit(indexMetProFit)*scaling; metaboliteTable{numberOfMet+4,indexTable} = [num2str(allMeanProFitMain,'%.1f'), plusMinusSign, num2str(allStdProFitMain,'%.1f')];
end metaboliteTable{numberOfMet+4,indexTable+1} = [num2str(allMeanLCModelMain,'%.1f'), plusMinusSign, num2str(allStdLCModelMain,'%.1f')];
if strcmp(metabolitesProFit(indexMetabolite),'Leu') end
fittedMetConcProFit = fittedMetConcProFit *1e8;
end function [allSimulMetConc, allLCModelMetConc, allProFitMetConc, allLCModelMetConcDev, allProFitMetConcDev] = ...
allLCModelMetConc(:, indexMetabolite) = fittedMetConcLCModel; reorganizeMetConcentrationsToMatrices(metabolites, metabolitesLCModel, metabolitesProFit, ...
allProFitMetConc(:, indexMetabolite) = fittedMetConcProFit; concentrationsRm, concentrationsLCModel, concentrationsProFit, activeMetabolites, scalingOn)
allLCModelMetConcDev(:, indexMetabolite) = (simulatedMetConc-fittedMetConcLCModel)./simulatedMetConc.*100;
allProFitMetConcDev(:, indexMetabolite) = (simulatedMetConc-fittedMetConcProFit)./simulatedMetConc.*100; iterationProFit = 4;
if plotCorrelations numberOfMet = length(metabolites);
if emptyFigureIdsCorr allSimulMetConc = concentrationsRm;
figIdsCorr{indexMetabolite} = figure; allLCModelMetConc = zeros(size(allSimulMetConc));
end allProFitMetConc = zeros(size(allSimulMetConc));
figure(figIdsCorr{indexMetabolite}); allLCModelMetConcDev = zeros(size(allSimulMetConc));
hold on allProFitMetConcDev = zeros(size(allSimulMetConc));
scatter(simulatedMetConc, fittedMetConcLCModel); for indexMetabolite = 1:numberOfMet
scatter(simulatedMetConc, fittedMetConcProFit, 'x'); simulatedMetConc = concentrationsRm(:, indexMetabolite);
plot(simulatedMetConc,simulatedMetConc); indexMetSim = find(strcmp(metabolites,'tCr(CH3)')); %'MMB'
title(metabolitesToDisplay(indexMetabolite)) fittedMetConcLCModel = zeros(size(simulatedMetConc));
for indexFit = 1:length(concentrationsLCModel)
xlabel('Simulated concentrations {\boldmath$c$}$_{k}$ (mmol/kg)', 'Interpreter', 'latex') currentConcentrationsLCModel = concentrationsLCModel{indexFit};
ylabel('Fitted concentrations {\boldmath$c$}$_{k}$ (mmol/kg)', 'Interpreter', 'latex') indexMetLCModel = find(strcmp(currentConcentrationsLCModel(1,:),'Cr')); %'Leu'
legend('LCModel {\boldmath$c$}$_{k}$', 'ProFit {\boldmath$c$}$_{k}$', 'Identity Line', 'Location', 'Northwest', 'Interpreter', 'latex') RefConc = currentConcentrationsLCModel{2,indexMetLCModel};
set(gca, 'FontSize', 13) RefConcSim = concentrationsRm(indexFit,indexMetSim);
xl = xlim; if scalingOn
if xl(2) > max(simulatedMetConc) scaling = RefConcSim/RefConc;
xl(2) = max(simulatedMetConc); else
end scaling = 1;
xlim(xl);
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');
% BlandAltman(simulatedMetConc, fittedMetConcLCModel);
% title(metabolites(indexMetabolite));
% BlandAltman(simulatedMetConc, fittedMetConcProFit);
% title(metabolites(indexMetabolite));
end end
indexMetLCModel = find(strcmp(currentConcentrationsLCModel(1,:),metabolitesLCModel(indexMetabolite)));
fittedMetConcLCModel(indexFit) = currentConcentrationsLCModel{2,indexMetLCModel}*scaling;
end end
fittedMetConcProFit = zeros(size(simulatedMetConc));
% allLCModelMetConcDev = allLCModelMetConcDev - median(allLCModelMetConcDev,1, 'omitnan'); for indexFit = 1:length(concentrationsProFit)
% allProFitMetConcDev = allProFitMetConcDev - median(allProFitMetConcDev,1, 'omitnan'); currentConcentrationsProFit = concentrationsProFit{indexFit}{iterationProFit};
if plotPrecision indexMetProFit = find(strcmp(activeMetabolites{iterationProFit},'Cr')); %'Leu'
yLimValue = 100; RefConc = currentConcentrationsProFit(indexMetProFit);
if isempty(figIds) RefConcSim = concentrationsRm(indexFit,indexMetSim);
% figure('Position',[612,509,1132,469],'OuterPosition',[604,501,1148,562], 'Units','pixels') if scalingOn
% figure('Position',[100,275,890,680],'Units','pixels') scaling = RefConcSim/RefConc;
% figIds{1} = subplot(2,1,2); else
% figIds{2} = subplot(2,1,1);%, 'Position', [0.58,0.16,0.35,0.76], 'Position', [0.13,0.16,0.35,0.76] scaling = 1;
%
figure('Position',[-908,-589,890,1400],'Units','pixels')
figIds{1} = subplot(4,1,2);
figIds{2} = subplot(4,1,1);
figIds{3} = subplot(4,1,4);
figIds{4} = subplot(4,1,3);
end end
positionsTicks = [2.2:1.5:1.5*numberOfMet+1.5]; indexMetProFit = find(strcmp(activeMetabolites{iterationProFit},metabolitesProFit(indexMetabolite)));
positions = positionsTicks + offsetPlot; fittedMetConcProFit(indexFit) = currentConcentrationsProFit(indexMetProFit)*scaling;
axes(figIds{1 + secondaryFigures})
hold on
boxPlotLCModel = boxplot(allLCModelMetConcDev, metabolitesLabels,'colors',plotColors,'symbol','+', 'positions',positions,'width',0.18);
xticks(positionsTicks)
xticklabels(metabolitesLabels)
xtickangle(45)
xlim([1 27.5])
title('LCModel')
ylim([-yLimValue,yLimValue]);
xlim([positionsTicks(1)-1, positionsTicks(end)+1])
set(gca, 'FontSize', 11)
ylabel('$Concentration\,\,change\,\,c^\%_{k}\,(\%)$', 'FontSize', 13, 'Interpreter', 'latex')
set(boxPlotLCModel(:,:),'linewidth',1);
yline(0,':', 'Color',[0.5 0.5 0.5]);
%%
axes(figIds{2 + secondaryFigures})
hold on
boxPlotProFit = boxplot(allProFitMetConcDev, metabolitesLabels,'colors',plotColors,'symbol','+', 'positions',positions,'width',0.18);
xticks(positionsTicks)
xticklabels(metabolitesLabels)
xtickangle(45)
xlim([1 27.5])
title('ProFit')
ylim([-yLimValue,yLimValue]);
set(gca, 'FontSize', 11)
ylabel('$Concentration\,\,change\,\,c^\%_{k}\,(\%)$', 'FontSize', 13, 'Interpreter', 'latex')
set(boxPlotProFit(:,:),'linewidth',1);
yline(0,':', 'Color',[0.5 0.5 0.5]);
end end
if strcmp(metabolitesProFit(indexMetabolite),'Leu')
fittedMetConcProFit = fittedMetConcProFit *1e8;
end
allLCModelMetConc(:, indexMetabolite) = fittedMetConcLCModel;
allProFitMetConc(:, indexMetabolite) = fittedMetConcProFit;
allLCModelMetConcDev(:, indexMetabolite) = (simulatedMetConc-fittedMetConcLCModel)./simulatedMetConc.*100;
allProFitMetConcDev(:, indexMetabolite) = (simulatedMetConc-fittedMetConcProFit)./simulatedMetConc.*100;
end
end
function figIdsCorr = plotCorrelationFigs(concentrationsRm, allLCModelMetConc, allProFitMetConc,...
metabolitesToDisplay, numberOfMet, dataExportPathBase, paramKeyword, truncSuffix, figIdsCorr)
if isempty(figIdsCorr)
emptyFigureIdsCorr = true;
figIdsCorr = cell(1,numberOfMet);
else
emptyFigureIdsCorr = false;
end
for indexMetabolite = 1:numberOfMet
simulatedMetConc = concentrationsRm(:, indexMetabolite);
fittedMetConcLCModel = allLCModelMetConc(:, indexMetabolite);
fittedMetConcProFit = allProFitMetConc(:, indexMetabolite);
if emptyFigureIdsCorr
figIdsCorr{indexMetabolite} = figure;
end
figure(figIdsCorr{indexMetabolite});
hold on
scatter(simulatedMetConc, fittedMetConcLCModel);
scatter(simulatedMetConc, fittedMetConcProFit, 'x');
plot(simulatedMetConc,simulatedMetConc);
title(metabolitesToDisplay(indexMetabolite))
display([paramKeyword, ' NANs:', num2str(sum(isnan(allLCModelMetConcDev)))]); xlabel('Simulated concentrations {\boldmath$c$}$_{k}$ (mmol/kg)', 'Interpreter', 'latex')
meanConcDevLCModel = mean(allLCModelMetConcDev,'omitnan'); ylabel('Fitted concentrations {\boldmath$c$}$_{k}$ (mmol/kg)', 'Interpreter', 'latex')
stdConcDevLCModel = std(allLCModelMetConcDev,'omitnan'); legend('LCModel {\boldmath$c$}$_{k}$', 'ProFit {\boldmath$c$}$_{k}$', 'Identity Line', 'Location', 'Northwest', 'Interpreter', 'latex')
display([paramKeyword, ' NANs ProFit:', num2str(sum(isnan(allProFitMetConcDev)))]); set(gca, 'FontSize', 13)
meanConcDevProFit = mean(allProFitMetConcDev,'omitnan'); xl = xlim;
stdConcDevProFit = std(allProFitMetConcDev,'omitnan'); if xl(2) > max(simulatedMetConc)
xl(2) = max(simulatedMetConc);
allMeanLCModel = mean(abs(meanConcDevLCModel));
allStdLCModel = mean(abs(stdConcDevLCModel));
allMeanProFit = mean(abs(meanConcDevProFit));
allStdProFit = mean(abs(stdConcDevProFit));
allMeanLCModelMain = mean(abs(meanConcDevLCModel(indexesMainMet)));
allStdLCModelMain = mean(abs(stdConcDevLCModel(indexesMainMet)));
allMeanProFitMain = mean(abs(meanConcDevProFit(indexesMainMet)));
allStdProFitMain = mean(abs(stdConcDevProFit(indexesMainMet)));
plusMinusSign = char(177);
metaboliteTable{2,indexTable} = 'ProFit';
metaboliteTable{2,indexTable+1} = 'LCModel';
for indexMet = 1:numberOfMet
metaboliteTable{indexMet+2,indexTable} = [num2str(meanConcDevProFit(indexMet),'%.1f'), plusMinusSign, num2str(stdConcDevProFit(indexMet),'%.1f')];
metaboliteTable{indexMet+2,indexTable+1} = [num2str(meanConcDevLCModel(indexMet),'%.1f'), plusMinusSign, num2str(stdConcDevLCModel(indexMet),'%.1f')];
end end
xlim(xl);
metaboliteTable{numberOfMet+3,indexTable} = [num2str(allMeanProFit,'%.1f'), plusMinusSign, num2str(allStdProFit,'%.1f')]; pathName = [dataExportPathBase, paramKeyword, '/correlations/'];
metaboliteTable{numberOfMet+3,indexTable+1} = [num2str(allMeanLCModel,'%.1f'), plusMinusSign, num2str(allStdLCModel,'%.1f')]; if ~exist(pathName, 'dir')
mkdir(pathName);
metaboliteTable{numberOfMet+4,indexTable} = [num2str(allMeanProFitMain,'%.1f'), plusMinusSign, num2str(allStdProFitMain,'%.1f')]; end
metaboliteTable{numberOfMet+4,indexTable+1} = [num2str(allMeanLCModelMain,'%.1f'), plusMinusSign, num2str(allStdLCModelMain,'%.1f')]; fileName = [metabolitesToDisplay{indexMetabolite}, '_', paramKeyword, truncSuffix];
saveas(figIdsCorr{indexMetabolite}, [pathName, fileName, '.tif']);
savefig(figIdsCorr{indexMetabolite}, [pathName,fileName, '.fig'],'compact');
end
end
function figIds = plotPrecisionFigs(figIds, numberOfMet, offsetPlot, secondaryFigures, plotColors, ...
allLCModelMetConcDev, allProFitMetConcDev, metabolitesLabels)
yLimValue = 100;
if isempty(figIds)
% figure('Position',[612,509,1132,469],'OuterPosition',[604,501,1148,562], 'Units','pixels')
% figure('Position',[100,275,890,680],'Units','pixels')
% figIds{1} = subplot(2,1,2);
% figIds{2} = subplot(2,1,1);%, 'Position', [0.58,0.16,0.35,0.76], 'Position', [0.13,0.16,0.35,0.76]
%
figure('Position',[-908,-589,890,1400],'Units','pixels')
figIds{1} = subplot(4,1,2);
figIds{2} = subplot(4,1,1);
figIds{3} = subplot(4,1,4);
figIds{4} = subplot(4,1,3);
end
positionsTicks = [2.2:1.5:1.5*numberOfMet+1.5];
positions = positionsTicks + offsetPlot;
axes(figIds{1 + secondaryFigures})
hold on
boxPlotLCModel = boxplot(allLCModelMetConcDev, metabolitesLabels,'colors',plotColors,'symbol','+', 'positions',positions,'width',0.18);
xticks(positionsTicks)
xticklabels(metabolitesLabels)
xtickangle(45)
xlim([1 27.5])
title('LCModel')
ylim([-yLimValue,yLimValue]);
xlim([positionsTicks(1)-1, positionsTicks(end)+1])
set(gca, 'FontSize', 11)
ylabel('$Concentration\,\,change\,\,c^\%_{k}\,(\%)$', 'FontSize', 13, 'Interpreter', 'latex')
set(boxPlotLCModel(:,:),'linewidth',1);
yline(0,':', 'Color',[0.5 0.5 0.5]);
%%
axes(figIds{2 + secondaryFigures})
hold on
boxPlotProFit = boxplot(allProFitMetConcDev, metabolitesLabels,'colors',plotColors,'symbol','+', 'positions',positions,'width',0.18);
xticks(positionsTicks)
xticklabels(metabolitesLabels)
xtickangle(45)
xlim([1 27.5])
title('ProFit')
ylim([-yLimValue,yLimValue]);
set(gca, 'FontSize', 11)
ylabel('$Concentration\,\,change\,\,c^\%_{k}\,(\%)$', 'FontSize', 13, 'Interpreter', 'latex')
set(boxPlotProFit(:,:),'linewidth',1);
yline(0,':', 'Color',[0.5 0.5 0.5]);
end end
function [metaboliteTable, indexTable] = setupTable(numberOfMet, numOfParameters, metabolitesLabels) function [metaboliteTable, indexTable] = setupTable(numberOfMet, numOfParameters, metabolitesLabels)
......
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