From 953b56db0a5f13c6fb0770c7cdb339727225fa04 Mon Sep 17 00:00:00 2001
From: Tamas Borbath <tamas.borbath@tuebingen.mpg.de>
Date: Thu, 25 Mar 2021 10:28:05 +0100
Subject: [PATCH] Visualization changes in files from createTestData
---
createTestData/createSimulatedSpectra.m | 42 ++++++++++++-------
.../evaluateProFitFittingParameters.m | 4 +-
createTestData/plotSimulationResults.m | 18 ++++----
createTestData/plot_all_test_data_profit.m | 16 +++++--
4 files changed, 52 insertions(+), 28 deletions(-)
diff --git a/createTestData/createSimulatedSpectra.m b/createTestData/createSimulatedSpectra.m
index 5e2a1dc..a287c53 100644
--- a/createTestData/createSimulatedSpectra.m
+++ b/createTestData/createSimulatedSpectra.m
@@ -140,8 +140,10 @@ conc_std_factor = zeros(1,numMetabolites);
current_pc0, current_pc1, current_df2, current_gm, current_em_std_factor, conc_std_factor, noiseVector, ...
truncPoint, saveData, 'meanConc', [], dwellTime * 1e3, scanFrequency, dataExportPathBase, water_ppm, scalingFactorRefPeak);
-figure(2);
-subplot(3,4,7:8)
+figure(1);
+subplot(5,4,8+7:8+8)
+% figure(2);
+% subplot(3,4,7:8)
plot(ppmVector,real(fftshift(fft(defaultSummedFid))));
%% generate the series of different concentrations
@@ -208,7 +210,8 @@ dataExportPath = [dataExportPathBase, paramKeyword, '\'];
concentrationsRm = zeros(length(gaussianValues), numMetabolites);
figure(1);
-subplot(2,4,5:6)
+subplot(5,4,5:6)
+% subplot(2,4,5:6)
for indexParam = 1:length(gaussianValues)
current_gm = gaussianValues(indexParam);
@@ -237,7 +240,8 @@ dataExportPath = [dataExportPathBase, paramKeyword, '\'];
concentrationsRm = zeros(length(pc0), numMetabolites);
figure(1);
-subplot(2,4,1:2)
+subplot(5,4,1:2)
+% subplot(2,4,1:2)
for indexParam = 1:length(pc0)
current_pc0 = pc0(indexParam);
@@ -265,7 +269,8 @@ dataExportPath = [dataExportPathBase, paramKeyword, '\'];
concentrationsRm = zeros(length(pc1), numMetabolites);
figure(1);
-subplot(2,4,3:4)
+subplot(5,4,3:4)
+% subplot(2,4,3:4)
for indexParam = 1:length(pc1)
current_pc1 = pc1(indexParam);
@@ -292,8 +297,10 @@ paramKeyword = 'df2_local';
dataExportPath = [dataExportPathBase, paramKeyword, '\'];
concentrationsRm = zeros(length(df2_local_scale), numMetabolites);
-figure(2);
-subplot(3,4,1:2)
+figure(1);
+subplot(5,4,8+1:8+2)
+% figure(2);
+% subplot(3,4,1:2)
for indexParam = 1:length(df2_local_scale)
for indexMetabolite = 1:numMetabolites
@@ -337,7 +344,8 @@ dataExportPath = [dataExportPathBase, paramKeyword, '\'];
concentrationsRm = zeros(length(df2_global), numMetabolites);
figure(1);
-subplot(2,4,7:8)
+subplot(5,4,7:8)
+% subplot(2,4,7:8)
for indexParam = 1:length(df2_global)
for indexMetabolite = 1:numMetabolites
current_df2(indexMetabolite) = df2_global(indexParam);
@@ -365,8 +373,10 @@ paramKeyword = 'em';
dataExportPath = [dataExportPathBase, paramKeyword, '\'];
concentrationsRm = zeros(length(df2_global), numMetabolites);
-figure(2);
-subplot(3,4,3:4)
+figure(1);
+subplot(5,4,8+3:8+4)
+% figure(2);
+% subplot(3,4,3:4)
for indexParam = 1:length(df2_global)
for indexMetabolite = 1:numMetabolites
% generate a random number between [-stdLim; stdLim]
@@ -409,8 +419,10 @@ paramKeyword = 'noise';
dataExportPath = [dataExportPathBase, paramKeyword, '\'];
concentrationsRm = zeros(length(noiseLevel), numMetabolites);
-figure(2);
-subplot(3,4,5:6)
+figure(1);
+subplot(5,4,8+5:8+6)
+% figure(2);
+% subplot(3,4,5:6)
for indexParam = 1:length(noiseLevel)
noiseVector = wgn(1,nTimepoints, noiseLevel(indexParam));
[summedFid, summedFidWithNoise, current_em, currentConcentrationRm] = createSummedSpectrum(...
@@ -441,8 +453,10 @@ prefixBaseline = 'Baseline_';
baselines = {'1Flat_drop_H20'; '2Flat'; '3Flat'; '4Flat'; '5Wildish'; '6Wildish'; '7Very_wild';...
'8Very_wild'; '9Wild'; '10Wild'; '11Wildish'; '12Wildish'; '13Normal'; '14Lipid_1.3'; '15Lipid_1.3_phased'; '16Zero'};
-figure(2);
-subplot(3,4,10:11)
+figure(1);
+subplot(5,4,8+10:8+11)
+% figure(2);
+% subplot(3,4,10:11)
for indexParam = 1:length(baselines)
baselineFileName = strcat(prefixBaseline, baselines{indexParam});
[currentBaseline, ~, ~, ~, ~] = ImportLCModelBasis(baselinesPath, baselineFileName, plotBasis, '1H');
diff --git a/createTestData/evaluateProFitFittingParameters.m b/createTestData/evaluateProFitFittingParameters.m
index 5766a57..df93d77 100644
--- a/createTestData/evaluateProFitFittingParameters.m
+++ b/createTestData/evaluateProFitFittingParameters.m
@@ -4,8 +4,8 @@ folderName = 'final_simulations';
exportFolder = {'11 Simulations'};
pathNameExport = 'ProFit test data';
pathBaseExportFiles = pathToDataFolder(pathNameExport, exportFolder);
-pathBaseExportFiles = pathBaseExportFiles(1:end-1);
-pathBaseExportFiles = [pathBaseExportFiles ' - R3\'];
+% pathBaseExportFiles = pathBaseExportFiles(1:end-1);
+% pathBaseExportFiles = [pathBaseExportFiles ' - R3\'];
dataExportPathBase = strcat(pathBaseExportFiles, exportFolder{1}, '\');
truncSuffix = '_truncOn';
folderFigures = [pathBaseExportFiles 'Output\' folderName, truncSuffix, '\'];
diff --git a/createTestData/plotSimulationResults.m b/createTestData/plotSimulationResults.m
index 9dd3413..fde9ce3 100644
--- a/createTestData/plotSimulationResults.m
+++ b/createTestData/plotSimulationResults.m
@@ -423,14 +423,14 @@ 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'};
+metabolitesFigureMain = {'NAA(CH_2)', 'tCr(CH_2)', 'tCho+','Gly','Glu','Gln',...
+ 'Asp', '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'};
+metabolitesFigureSupporting = {'tCr(CH_3)', 'mI', 'sI', 'NAA(CH_3)','Tau'};
figID_Supporting = figure();
supportingFigureRunningIndex = 0;
@@ -490,21 +490,21 @@ for indexMetabolite = 1:numberOfMet
fittedMetConcProFit = fittedMetConcProFit *1e-7;
end
hold on
- scatter(simulatedMetConc, fittedMetConcLCModel, 'MarkerEdgeColor', colorLCModel);
- scatter(simulatedMetConc, fittedMetConcProFit, 'x', 'MarkerEdgeColor', colorProFit);
+ scatter(simulatedMetConc, fittedMetConcLCModel, 15, 'MarkerEdgeColor', colorLCModel);
+ scatter(simulatedMetConc, fittedMetConcProFit, 15, '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))
if plotXLabel
- xlabel('$c_{k}^{simulated} \,\, (mmol/kg)$', 'Interpreter', 'latex')
+ xlabel('$c_{k}^{simulated} \,\, (mmol/kg)$', 'Interpreter', 'latex','FontSize', 10)
end
if plotYLabel
- ylabel('$c_k^{fitted} \,\, (mmol/kg)$', 'Interpreter', 'latex')
+ ylabel('$c_k^{fitted} \,\, (mmol/kg)$', 'Interpreter', 'latex','FontSize', 10)
end
- legend('$LCModel \,\, c_k^{fitted}$', '$ProFit \,\, c_k^{fitted}$', '$Identity \, Line$', 'Location', 'best', 'Interpreter', 'latex')
- set(gca, 'FontSize', 13)
+ 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)])
diff --git a/createTestData/plot_all_test_data_profit.m b/createTestData/plot_all_test_data_profit.m
index d7b90a9..bba246e 100644
--- a/createTestData/plot_all_test_data_profit.m
+++ b/createTestData/plot_all_test_data_profit.m
@@ -179,17 +179,27 @@ rpc_table{end,1} = 'Mean';
%title('Reproducibility');
subplotsX = 4;
subplotsY = 4;
-totalSubplots = subplotsX * subplotsY;
+totalSubplots1 = subplotsX * subplotsY;
rpcSum = zeros(1,numberOfMet);
diffMedian = zeros(1,numberOfMet);
for indexMet = 1: numberOfMet
if indexMet == metaboliteRef
continue;
end
- if mod(indexMet,totalSubplots/2) == 1
+ if (indexMet == 1) || (indexMet == totalSubplots1/2+1)
figure;
+ if indexMet >= 8
+ subplotsX = 6;
+ subplotsY = 3;
+ totalSubplots = subplotsX * subplotsY;
+ end
+ end
+ if indexMet <= totalSubplots1/2
+ runningIndexPlot = (indexMet-1)+1+floor((indexMet-1)/subplotsY)*subplotsY-floor((indexMet-1)/totalSubplots1*2)*totalSubplots1;
+ else
+ indexMet2 = indexMet - totalSubplots1/2;
+ runningIndexPlot = (indexMet2-1)+1+floor((indexMet2-1)/subplotsY)*subplotsY-floor((indexMet2-1)/totalSubplots*2)*totalSubplots;
end
- runningIndexPlot = (indexMet-1)+1+floor((indexMet-1)/subplotsY)*subplotsY-floor((indexMet-1)/totalSubplots*2)*totalSubplots;
%ProFit Concentrations
metConcAllSubjProFitScaled_ = metConcAllSubjProFitScaled(:, :, indexMet);
--
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