Added also small metabolites to plot_all_test_data_profit

createTestData/plot_all_test_data_profit.m

@@ -28,7 +28,7 @@ pathNameExport = 'ProFit test data';
 pathBaseExportFiles = pathToDataFolder(pathNameExport, exportFolders);
 
 pathBaseExportFiles = pathBaseExportFiles(1:end-1);
-pathBaseExportFiles = [pathBaseExportFiles ' - R3\'];
+pathBaseExportFiles = [pathBaseExportFiles ' - R3_new\'];
 
 dataExportPathBaseRef = strcat(pathBaseExportFiles, exportFolders{2}, '\');
 dataExportPathBase = strcat(pathBaseExportFiles, exportFolders{reconOption+1}, '\');
@@ -165,16 +165,17 @@ numOfSimulations = length(namingSuffixesAve)*length(namingSuffixesCoil);
 %     'corrInfo',corrinfo,'baInfo',BAinfo,'axesLimits',limits,'showFitCI',' on',...
 %     'baStatsMode','Gaussian','forceZeroIntercept','on', 'diffValueMode', 'percent');
 
-rpc_table = cell(numberOfMet+5,5);
+rpc_table = cell(numberOfMet+6,5);
 rpc_table{1,2} = softwareNames{1};
 rpc_table{1,4} = softwareNames{2};
 rpc_table{2,2} = subsets_refit{1};
 rpc_table{2,3} = subsets_refit{2};
 rpc_table{2,4} = subsets_refit{1};
 rpc_table{2,5} = subsets_refit{2};
-rpc_table(3:end-3,1) = metabolitesToDisplay;
+rpc_table(3:end-4,1) = metabolitesToDisplay;
+rpc_table{end-2,1} = 'Mean';
 rpc_table{end-1,1} = 'Mean Main';
-rpc_table{end,1} = 'Mean';
+rpc_table{end,1} = 'Mean Small';
     
 %title('Reproducibility');
 subplotsX = 4;
@@ -282,23 +283,39 @@ for indexMet = 1: numberOfMet
 end
 
 rpc_values = cell2mat(rpc_table(3:end-3,2:5));
+% extract summaries main met
 rpc_meanProFit_32ave_main = mean(rpc_values(indecesMainMet,1));
 rpc_meanProFit_64ave_main = mean(rpc_values(indecesMainMet,2));
 rpc_meanLCModel_32ave_main = mean(rpc_values(indecesMainMet,3));
 rpc_meanLCModel_64ave_main = mean(rpc_values(indecesMainMet,4));
-rpc_table(3:end-3,2:5) = sprintfc('%.0f',rpc_values);
-rpc_table{end-1,2} = num2str(rpc_meanProFit_32ave_main, '%.0f');
-rpc_table{end-1,3} = num2str(rpc_meanProFit_64ave_main, '%.0f');
-rpc_table{end-1,4} = num2str(rpc_meanLCModel_32ave_main, '%.0f');
-rpc_table{end-1,5} = num2str(rpc_meanLCModel_64ave_main, '%.0f');
+% extract summaries small met
+rpc_meanProFit_32ave_small = mean(rpc_values(~indecesMainMet,1));
+rpc_meanProFit_64ave_small = mean(rpc_values(~indecesMainMet,2));
+rpc_meanLCModel_32ave_small = mean(rpc_values(~indecesMainMet,3));
+rpc_meanLCModel_64ave_small = mean(rpc_values(~indecesMainMet,4));
+% extract summaries all met
 rpc_meanProFit_32ave = mean(rpc_values(:,1));
 rpc_meanProFit_64ave = mean(rpc_values(:,2));
 rpc_meanLCModel_32ave = mean(rpc_values(:,3));
 rpc_meanLCModel_64ave = mean(rpc_values(:,4));
-rpc_table{end,2} = num2str(rpc_meanProFit_32ave, '%.0f');
-rpc_table{end,3} = num2str(rpc_meanProFit_64ave, '%.0f');
-rpc_table{end,4} = num2str(rpc_meanLCModel_32ave, '%.0f');
-rpc_table{end,5} = num2str(rpc_meanLCModel_64ave, '%.0f');
+%% Add to RPC_table: all met
+rpc_table(3:end-4,2:5) = sprintfc('%.0f',rpc_values);
+% Add to RPC_table: mean values
+rpc_table{end-2,2} = num2str(rpc_meanProFit_32ave, '%.0f');
+rpc_table{end-2,3} = num2str(rpc_meanProFit_64ave, '%.0f');
+rpc_table{end-2,4} = num2str(rpc_meanLCModel_32ave, '%.0f');
+rpc_table{end-2,5} = num2str(rpc_meanLCModel_64ave, '%.0f');
+% Add to RPC_table: mean main met
+rpc_table{end-1,2} = num2str(rpc_meanProFit_32ave_main, '%.0f');
+rpc_table{end-1,3} = num2str(rpc_meanProFit_64ave_main, '%.0f');
+rpc_table{end-1,4} = num2str(rpc_meanLCModel_32ave_main, '%.0f');
+rpc_table{end-1,5} = num2str(rpc_meanLCModel_64ave_main, '%.0f');
+% Add to RPC_table: mean small met
+rpc_table{end,2} = num2str(rpc_meanProFit_32ave_small, '%.0f');
+rpc_table{end,3} = num2str(rpc_meanProFit_64ave_small, '%.0f');
+rpc_table{end,4} = num2str(rpc_meanLCModel_32ave_small, '%.0f');
+rpc_table{end,5} = num2str(rpc_meanLCModel_64ave_small, '%.0f');
+%write file
 xlswrite([pathBaseExportFiles, 'InVivoResults_RPC.xlsx'], rpc_table)
 
 %% code will break here. This used to be the old style plotting/results without Bland-Altman plots.
@@ -312,10 +329,15 @@ mainMetaboliteConcentrationsAllSubj = metaboliteConcentrationsAllSubjNorm(:, ind
 meanMainMetDeviation = mean(abs(mainMetaboliteConcentrationsAllSubj(:)), 'omitnan');
 stdMainMetDeviation  = std(abs(mainMetaboliteConcentrationsAllSubj(:)), 'omitnan');
 
+smallMetaboliteConcentrationsAllSubj = metaboliteConcentrationsAllSubjNorm(:, ~indecesMainMet);
+meanSmallMetDeviation = mean(abs(smallMetaboliteConcentrationsAllSubj(:)), 'omitnan');
+stdSmallMetDeviation  = std(abs(smallMetaboliteConcentrationsAllSubj(:)), 'omitnan');
+
 metaboliteTable = cell(numberOfMet+3,2);
 metaboliteTable(2:numberOfMet+1,1) = metabolitesLabels;
 metaboliteTable{numberOfMet+2,1}   = 'Mean';
 metaboliteTable{numberOfMet+3,1}   = 'Mean Main Metabolites';
+metaboliteTable{numberOfMet+4,1}   = 'Mean Small Metabolites';
 
 plusMinusSign = char(177);
 metaboliteTable{1,2} = SoftwareName;
@@ -326,6 +348,7 @@ end
 
 metaboliteTable{numberOfMet+2,2}   = [num2str(meanAllMetDeviation,'%.1f'),  plusMinusSign, num2str(stdAllMetDeviation,'%.1f')];
 metaboliteTable{numberOfMet+3,2}   = [num2str(meanMainMetDeviation,'%.1f'),  plusMinusSign, num2str(stdMainMetDeviation,'%.1f')];
+metaboliteTable{numberOfMet+3,2}   = [num2str(meanSmallMetDeviation,'%.1f'),  plusMinusSign, num2str(stdSmallMetDeviation,'%.1f')];
 
 xlswrite([pathBaseExportFiles, 'InVivoResults' SoftwareName, '.xlsx'], metaboliteTable)
 %