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Commit 0e65526e authored by Tamas Borbath's avatar Tamas Borbath
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Changed plot orientation and added correlation plots for Glx

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createTestData/plotSimulationResults.m
+ 149
− 51
View file @ 0e65526e
......@@ -5,7 +5,7 @@ exportFolder = {'11 Simulations'};
pathNameExport = 'ProFit test data';
pathBaseExportFiles = pathToDataFolder(pathNameExport, exportFolder);
pathBaseExportFiles = pathBaseExportFiles(1:end-1);
pathBaseExportFiles = [pathBaseExportFiles ' - R3\'];
pathBaseExportFiles = [pathBaseExportFiles ' - R3_new\'];
dataExportPathBase = strcat(pathBaseExportFiles, exportFolder{1}, '\');
truncSuffix = '_truncOn';
scalingOn = true;
......@@ -138,17 +138,19 @@ sumAllStdProFitMain = sumAllStdProFitMain + allStdProFitMain;
%% -----------------------------------------------------------------------------------------------------------
axes(figIds{1})
str = {'$$\varphi_0$$', '$$\varphi_1$$', '$$\omega_{global}$$', '{\boldmath$\omega_{local}$}'};
xOffset = 0.65;
yOffsetRect = 0.085; %0.075; -for two subfigures
% xOffset = 0.65;
xOffset = 0.38; %Revision 1
yOffsetRect = 0.080; %0.085 - submission 1 %0.075; -for two subfigures
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
yOffset = 0.87;% Revision 1
annotation('textbox',[xOffset yOffset 0.1 0.1],'String',str{indexSim},'FitBoxToText','On', ...
'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})
yOffset = 0.612;% 4 subfigs%0.37; - Two figs placed lower%0.37 -Two figs
annotation('textbox',[xOffset yOffset 0.1 0.1],'String',str{indexSim},'FitBoxToText','On', ...
'EdgeColor','none', 'FontSize', 12, 'FontWeight','bold', 'Interpreter','latex','Color',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
% annotation('textbox',[xOffset yOffset 0.1 0.1],'String',str{indexSim},'FitBoxToText','On', ...
% 'EdgeColor','none', 'FontSize', 12, 'FontWeight','bold', 'Interpreter','latex','Color',plotColors{indexSim})
% annotation('rectangle',[xOffset-0.012 yOffset+yOffsetRect 0.01 0.01],'EdgeColor','none', 'FaceColor',plotColors{indexSim})
xOffset = xOffset + 0.004*length(str{indexSim});
end
......@@ -157,8 +159,9 @@ xlswrite([dataExportPathBase, 'SimulationsTable1.xlsx'],metaboliteTable);
numOfParameters2 = 5;
[metaboliteTable, indexTable] = setupTable(numberOfMet, numOfParameters2, metabolitesLabels);
% figIds = [];
figIds = [];
secondaryFigures = 2;
secondaryFigures = 0;
%% -----------------------------------------------------------------------------------------------------------
%%
paramKeyword = 'gauss';
......@@ -286,17 +289,19 @@ sumAllStdProFitMain = sumAllStdProFitMain / (numOfParameters + numOfParameters
axes(figIds{1})
str = {'$$\nu_g$$', '{\boldmath$\nu_{e}$}', '{\boldmath$noise$}', '{\boldmath$baseline$}'};
stringLenghts = {13, 13, 19, 27};
xOffset = 0.63;
yOffsetRect = 0.085; %0.075; -for two subfigures
% xOffset = 0.63;
xOffset = 0.38; %Revision 1
yOffsetRect = 0.080; %0.085 - submission 1 %0.075; -for two subfigures
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
yOffset = 0.87;% Revision 1
annotation('textbox',[xOffset yOffset 0.1 0.1],'String',str{indexSim},'FitBoxToText','On', ...
'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})
yOffset = 0.172;% 4 subfigs%0.37; - Two figs placed lower%0.37 -Two figs
annotation('textbox',[xOffset yOffset 0.1 0.1],'String',str{indexSim},'FitBoxToText','On', ...
'EdgeColor','none', 'FontSize', 12, 'FontWeight','bold', 'Interpreter','latex','Color',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
% annotation('textbox',[xOffset yOffset 0.1 0.1],'String',str{indexSim},'FitBoxToText','On', ...
% 'EdgeColor','none', 'FontSize', 12, 'FontWeight','bold', 'Interpreter','latex','Color',plotColors{indexSim})
% annotation('rectangle',[xOffset-0.012 yOffset+yOffsetRect 0.01 0.01],'EdgeColor','none', 'FaceColor',plotColors{indexSim})
xOffset = xOffset + 0.004*stringLenghts{indexSim};
end
......@@ -341,6 +346,11 @@ allStdLCModelMain = mean(abs(stdConcDevLCModel(indexesMainMet)));
allMeanProFitMain = mean(abs(meanConcDevProFit(indexesMainMet)));
allStdProFitMain = mean(abs(stdConcDevProFit(indexesMainMet)));
allMeanLCModelSmall = mean(abs(meanConcDevLCModel(~indexesMainMet)));
allStdLCModelSmall = mean(abs(stdConcDevLCModel(~indexesMainMet)));
allMeanProFitSmall = mean(abs(meanConcDevProFit(~indexesMainMet)));
allStdProFitSmall = mean(abs(stdConcDevProFit(~indexesMainMet)));
plusMinusSign = char(177);
metaboliteTable{2,indexTable} = 'ProFit';
metaboliteTable{2,indexTable+1} = 'LCModel';
......@@ -354,6 +364,9 @@ metaboliteTable{numberOfMet+3,indexTable+1} = [num2str(allMeanLCModel,'%.1f'),
metaboliteTable{numberOfMet+4,indexTable} = [num2str(allMeanProFitMain,'%.1f'), plusMinusSign, num2str(allStdProFitMain,'%.1f')];
metaboliteTable{numberOfMet+4,indexTable+1} = [num2str(allMeanLCModelMain,'%.1f'), plusMinusSign, num2str(allStdLCModelMain,'%.1f')];
metaboliteTable{numberOfMet+5,indexTable} = [num2str(allMeanProFitSmall,'%.1f'), plusMinusSign, num2str(allStdProFitSmall,'%.1f')];
metaboliteTable{numberOfMet+5,indexTable+1} = [num2str(allMeanLCModelSmall,'%.1f'), plusMinusSign, num2str(allStdLCModelSmall,'%.1f')];
end
%% reorganize the fitted concentrations to 2D tables
......@@ -413,6 +426,12 @@ end
function figIdsCorr = plotCorrelationFigs(concentrationsRm, allLCModelMetConc, allProFitMetConc,...
metabolitesToDisplay, numberOfMet, dataExportPathBase, paramKeyword, truncSuffix, figIdsCorr)
%TODO should I have this here? I don't know
plotCorrelationsGlx(concentrationsRm, allLCModelMetConc, allProFitMetConc,...
metabolitesToDisplay,1:100);
plotCorrelationsGlx(concentrationsRm, allLCModelMetConc, allProFitMetConc,...
metabolitesToDisplay,1:5:100);
if isempty(figIdsCorr)
emptyFigureIdsCorr = true;
figIdsCorr = cell(1,numberOfMet);
......@@ -450,16 +469,23 @@ for indexMetabolite = 1:numberOfMet
figure(figID_Main);
mainFigureRunningIndex = mainFigureRunningIndex + 1;
subplot(figureMainRows, figureMainCols, mainFigureRunningIndex);
if mod(mainFigureRunningIndex,figureMainCols)== 1
% if mod(mainFigureRunningIndex,figureMainCols)== 1 %first submission. Label on every row
if mainFigureRunningIndex == 7 % Revision 1: Just one label
plotYLabel = true;
else
plotYLabel = false;
end
if round((mainFigureRunningIndex+1)/figureMainCols)== figureMainRows
% if round((mainFigureRunningIndex+1)/figureMainCols)== figureMainRows %first submission. Label on every column
if mainFigureRunningIndex == 11 %Revision 1: Just one label
plotXLabel = true;
else
plotXLabel = false;
end
if mainFigureRunningIndex == 3 %Revision 1: Just one legend
plotLegend = true;
else
plotLegend = false;
end
elseif sum(contains(metabolitesFigureSupporting, metabolitesToDisplay{indexMetabolite}))
figure(figID_Supporting);
supportingFigureRunningIndex = supportingFigureRunningIndex + 2;
......@@ -477,6 +503,11 @@ for indexMetabolite = 1:numberOfMet
else
plotXLabel = false;
end
if supportingFigureRunningIndex == 4 %Revision 1: Just one legend
plotLegend = true;
else
plotLegend = false;
end
else
warning('Metabolite not associated with either main or supporting figure: ', metabolitesToDisplay{indexMetabolite});
figure();
......@@ -498,13 +529,15 @@ for indexMetabolite = 1:numberOfMet
title(metabolitesToDisplay(indexMetabolite))
if plotXLabel
xlabel('$c_{k}^{simulated} \,\, (mmol/kg)$', 'Interpreter', 'latex','FontSize', 10)
xlabel('$\bf c_{k}^{simulated} \,\, (mmol/kg)$', 'Interpreter', 'latex','FontSize', 11)
end
if plotYLabel
ylabel('$c_k^{fitted} \,\, (mmol/kg)$', 'Interpreter', 'latex','FontSize', 10)
ylabel('$\bf c_k^{fitted} \,\, (mmol/kg)$', 'Interpreter', 'latex','FontSize', 11)
end
if plotLegend
handleLegend = legend('$LCModel \,\, c_k^{fitted}$', '$ProFit \,\, c_k^{fitted}$', '$Identity \, Line$', 'Location', 'best', 'Interpreter', 'latex', 'FontSize', 10);
title(handleLegend,'Legend', 'FontSize',10);
end
legend('$LCModel \,\, c_k^{fitted}$', '$ProFit \,\, c_k^{fitted}$', '$Identity \, Line$', 'Location', 'best', 'Interpreter', 'latex', 'FontSize', 8)
xlim([min(identityLine),max(identityLine)])
ylim([min(identityLine),max(identityLine)])
......@@ -529,43 +562,51 @@ function figIds = plotPrecisionFigs(figIds, numberOfMet, offsetPlot, secondaryFi
% 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);
%%Revision 1
% figure('Position',[612,509,1132,469],'OuterPosition',[604,501,1148,562], 'Units','pixels')
figure('Position',[9,10,1033,986],'Units','pixels')
figIds{1} = subplot(1,2,2);
figIds{2} = subplot(1,2,1);%, '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])
boxPlotLCModel = boxplot(allLCModelMetConcDev, metabolitesLabels,'colors',plotColors,'symbol','+', 'positions',positions,'width',0.18,'orientation', 'horizontal');
yticks(positionsTicks)
yticklabels(metabolitesLabels)
set(gca,'Ydir','reverse')
% xtickangle(45)
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')
xlim([-yLimValue,yLimValue]);
ylim([positionsTicks(1)-1, positionsTicks(end)+1])
set(gca, 'FontSize', 12)
set(gca, 'YAxisLocation', 'right')
xlabel('$Concentration\,\,change\,\,c^\%_{k}\,(\%)$', 'FontSize', 13, 'Interpreter', 'latex')
set(boxPlotLCModel(:,:),'linewidth',1);
yline(0,':', 'Color',[0.5 0.5 0.5]);
xline(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])
boxPlotProFit = boxplot(allProFitMetConcDev, metabolitesLabels,'colors',plotColors,'symbol','+', 'positions',positions,'width',0.18,'orientation', 'horizontal');
yticks(positionsTicks)
yticklabels(metabolitesLabels)
set(gca,'Ydir','reverse')
% ytickangle(45)
ylim([1 27.5])
title('ProFit')
ylim([-yLimValue,yLimValue]);
set(gca, 'FontSize', 11)
ylabel('$Concentration\,\,change\,\,c^\%_{k}\,(\%)$', 'FontSize', 13, 'Interpreter', 'latex')
xlim([-yLimValue,yLimValue]);
set(gca, 'FontSize', 12)
set(gca, 'YAxisLocation', 'left')
xlabel('$Concentration\,\,change\,\,c^\%_{k}\,(\%)$', 'FontSize', 13, 'Interpreter', 'latex')
set(boxPlotProFit(:,:),'linewidth',1);
yline(0,':', 'Color',[0.5 0.5 0.5]);
xline(0,':', 'Color',[0.5 0.5 0.5]);
end
%% setup the table to show metabolite concentration changes
......@@ -574,5 +615,62 @@ metaboliteTable = cell(numberOfMet+4,numOfParameters*2+1);
metaboliteTable(3:numberOfMet+2,1) = metabolitesLabels;
metaboliteTable{numberOfMet+3,1} = 'Mean';
metaboliteTable{numberOfMet+4,1} = 'Mean Main Metabolites';
metaboliteTable{numberOfMet+5,1} = 'Mean Small Metabolites';
indexTable = 0;
end
function plotCorrelationsGlx(concentrationsRm, allLCModelMetConc, allProFitMetConc,...
metabolitesToDisplay, subsample)
colorOriginal = [0 0 0];
colorProFit = [0.49 0.18 0.56];
colorLCModel = [0.85 0.33 0.1];
indexGlu = find(strcmp(metabolitesToDisplay, 'Glu'));
indexGln = find(strcmp(metabolitesToDisplay, 'Gln'));
simulatedGluConc = concentrationsRm(:, indexGlu);
simulatedGlnConc = concentrationsRm(:, indexGln);
fittedGluConcLCModel = allLCModelMetConc(:, indexGlu);
fittedGlnConcLCModel = allLCModelMetConc(:, indexGln);
fittedGluConcProFit = allProFitMetConc(:, indexGlu);
fittedGlnConcProFit = allProFitMetConc(:, indexGln);
% subsample = 1:5:100;
figure();
plotYLabel = true;
plotXLabel = true;
plotLegend = true;
scatterSize = 50;
fontSize = 14;
hold on
scatter(fittedGluConcLCModel(subsample), fittedGlnConcLCModel(subsample), scatterSize, 'd', 'MarkerEdgeColor', colorLCModel);
scatter(simulatedGluConc(subsample), simulatedGlnConc(subsample), scatterSize, 'o', 'MarkerEdgeColor', colorOriginal);
scatter(fittedGluConcProFit(subsample), fittedGlnConcProFit(subsample), scatterSize, 'x', 'MarkerEdgeColor', colorProFit);
for index = subsample
plot([fittedGluConcLCModel(index), simulatedGluConc(index), fittedGluConcProFit(index)],[fittedGlnConcLCModel(index), simulatedGlnConc(index), fittedGlnConcProFit(index)], 'color', colorOriginal);
end
offSetEnds = max(simulatedGluConc)*0.05;
identityLineGlu = min(simulatedGluConc)-offSetEnds:0.01:max(simulatedGluConc)+offSetEnds;
offSetEnds = max(simulatedGlnConc)*0.05;
identityLineGln = min(simulatedGlnConc)-offSetEnds:0.01:max(simulatedGlnConc)+offSetEnds;
set(gca, 'FontSize', fontSize)
if plotXLabel
xlabel('$c_{Glu} \,\, (mmol/kg)$', 'Interpreter', 'latex','FontSize', fontSize+2)
end
if plotYLabel
ylabel('$c_{Gln} \,\, (mmol/kg)$', 'Interpreter', 'latex','FontSize', fontSize+2)
end
if plotLegend
handleLegend = legend('$LCModel$', '$Simulated$', '$ProFit$', 'Location', 'best', 'Interpreter', 'latex', 'FontSize', fontSize-2);
title(handleLegend,'Legend');
end
xlim([min(identityLineGlu),max(identityLineGlu)])
ylim([min(identityLineGln),max(identityLineGln)])
end
\ No newline at end of file
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