Merge pull request #70 from MaxvandenBoom/master

Supplement Fig 3 y-axis now in ms, updates some script names and output folder; corrected p-values outputted for fig 6-7
MultimodalNeuroimagingLab · Feb 3, 2023 · faf1dff · faf1dff
2 parents 3e87b97 + 54d92ec
commit faf1dff
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diff --git a/README.md b/README.md
@@ -13,10 +13,10 @@ Scripts to process the data, detect N1 responses and add tract information:
 - scripts/ccep04_averageConnections.m
 
 Scripts to make the figure panels:
-- makeFig1A_plotMNI.m
+- makeFig1A_and_SupFig9_plotMNI.m
 - makeFig1B_subjectResponses.m
-- makeFig1C_heatmapResponsesAge.m
-- makeFig2and3_transmissionAcrossAge.m
+- makeFig1C_and_Fig3A_heatmaps.m
+- makeFig2_and_Fig3BC_transmissionAges.m
 
 
 To make all functions work, an m-file called personalDataPath.m should be stored in the root dir. This file should have the following content:

diff --git a/scripts/makeFig1A_plotMNI.m → scripts/makeFig1A_and_SupFig9_plotMNI.m b/scripts/makeFig1A_plotMNI.m → scripts/makeFig1A_and_SupFig9_plotMNI.m
@@ -1,5 +1,7 @@
 %
-% This script creates the images for Figure 1A that depict a MNI surface with tracts, subtracts, ROIs and electrodes
+% This script produces the images for:
+%    - Figure 1A - that depict a MNI surface with tracts, subtracts, ROIs and electrodes
+%    - Supplemental Figure 9 - distribution of electrodes over different age groups
 %
 % Max van den Boom, Jaap van der Aar, Giulio Castegnaro, Dora Hermes, Dorien van Blooijs, 2022
 %
@@ -275,7 +277,10 @@
         ieeg_viewLight(v_d(1), v_d(2))
 
         % save the image
-        figureName = fullfile(myDataPath.output, 'derivatives', 'render', ['leftMNIpial_', rois(iTr).tract_name, '_',  strrep(rois(iTr).sub_tract(iSubTr).name, '-', ''), '.png']);
+        if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+            mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
+        end
+        figureName = fullfile(myDataPath.output, 'derivatives', 'images', ['leftMNIpial_', rois(iTr).tract_name, '_',  strrep(rois(iTr).sub_tract(iSubTr).name, '-', ''), '.png']);
         set(gcf, 'PaperPositionMode', 'auto')
         set(hFig, 'Visible', 'on');
         print('-dpng', '-r300', figureName)
@@ -408,7 +413,11 @@
 figure(hFigElec);
 set(hFigElec, 'renderer', 'Painters')
 set(hFigElec, 'PaperPositionMode', 'auto')
-figureName = fullfile(myDataPath.output, 'derivatives', 'age', 'SupFigS9_ElecCoverage');
+
+if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+    mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
+end
+figureName = fullfile(myDataPath.output, 'derivatives', 'images', 'SupFigS9_ElecCoverage');
 print('-dpng', '-r300', figureName)
 print('-depsc', '-r300', figureName)
 %close(hFigElec)
diff --git a/scripts/makeFig1B_subjectResponses.m b/scripts/makeFig1B_subjectResponses.m
@@ -72,10 +72,10 @@
                 %
                 % save
                 %
-                if ~exist(fullfile(myDataPath.output,'derivatives', 'age'), 'dir')
-                    mkdir(fullfile(myDataPath.output,'derivatives', 'age'));
+                if ~exist(fullfile(myDataPath.output,'derivatives', 'images'), 'dir')
+                    mkdir(fullfile(myDataPath.output,'derivatives', 'images'));
                 end
-                figureName = fullfile(myDataPath.output,'derivatives', 'age', ['CCEPexamples_6subjects', '_', rois(iTr).tract_name, '_', strrep(strSubTitle, ' -> ', '_')]);
+                figureName = fullfile(myDataPath.output,'derivatives', 'images', ['CCEPexamples_6subjects', '_', rois(iTr).tract_name, '_', strrep(strSubTitle, ' -> ', '_')]);
 
                 set(gcf, 'renderer', 'Painters')
                 set(gcf, 'PaperPositionMode', 'auto')

diff --git a/scripts/makeFig1Cand3A_heatmapResponsesAge.m → scripts/makeFig1C_and_Fig3A_heatmaps.m b/scripts/makeFig1Cand3A_heatmapResponsesAge.m → scripts/makeFig1C_and_Fig3A_heatmaps.m
@@ -108,10 +108,10 @@
                 %
                 % save
                 %
-                if ~exist(fullfile(myDataPath.output,'derivatives', 'age'), 'dir')
-                    mkdir(fullfile(myDataPath.output,'derivatives', 'age'));
+                if ~exist(fullfile(myDataPath.output,'derivatives', 'images'), 'dir')
+                    mkdir(fullfile(myDataPath.output,'derivatives', 'images'));
                 end
-                figureName = fullfile(myDataPath.output,'derivatives', 'age', ['sortedAge_tmax' int2str(ttmax * 1000), '_', rois(iTr).tract_name, '_', strrep(strSubTitle, ' -> ', '_')]);
+                figureName = fullfile(myDataPath.output,'derivatives', 'images', ['sortedAge_tmax' int2str(ttmax * 1000), '_', rois(iTr).tract_name, '_', strrep(strSubTitle, ' -> ', '_')]);
 
                 set(gcf, 'PaperPositionMode', 'auto')
                 print('-dpng', '-r300', figureName)

diff --git a/scripts/makeFig2and3_transmissionAcrossAge.m → ...ts/makeFig2_and_Fig3BC_transmissionAges.m b/scripts/makeFig2and3_transmissionAcrossAge.m → ...ts/makeFig2_and_Fig3BC_transmissionAges.m
@@ -368,10 +368,10 @@
             set(gca, 'YGrid', 'on', 'XGrid', 'off');
 
             % save latency figure
-            if ~exist(fullfile(myDataPath.output, 'derivatives', 'age'), 'dir')
-                mkdir(fullfile(myDataPath.output, 'derivatives', 'age'));
+            if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+                mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
             end
-            figureName = fullfile(myDataPath.output, 'derivatives', 'age', ['ageVsLatency', '_', rois(iTr).tract_name, '_', strrep(strSubTitle, ' -> ', '_')]);
+            figureName = fullfile(myDataPath.output, 'derivatives', 'images', ['ageVsLatency', '_', rois(iTr).tract_name, '_', strrep(strSubTitle, ' -> ', '_')]);
             set(gcf,'PaperPositionMode', 'auto');
             print('-dpng', '-r300', figureName);
             print('-depsc', '-r300', figureName);
@@ -432,7 +432,10 @@
             set(gca, 'YGrid', 'on', 'XGrid', 'off');
 
             % save speed figure
-            figureName = fullfile(myDataPath.output, 'derivatives', 'age', ['ageVsSpeed', '_', rois(iTr).tract_name, '_', strrep(strSubTitle, ' -> ', '_')]);
+            if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+                mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
+            end
+            figureName = fullfile(myDataPath.output, 'derivatives', 'images', ['ageVsSpeed', '_', rois(iTr).tract_name, '_', strrep(strSubTitle, ' -> ', '_')]);
             set(gcf,'PaperPositionMode', 'auto');
             print('-dpng', '-r300', figureName);
             print('-depsc', '-r300', figureName);

diff --git a/scripts/makeSupFig1_only8maSubs.m → scripts/makeSupFig1_currents.m b/scripts/makeSupFig1_only8maSubs.m → scripts/makeSupFig1_currents.m
@@ -199,11 +199,11 @@
 legend()
 
 % save
-if ~exist(fullfile(myDataPath.output, 'derivatives', 'age'), 'dir')
-    mkdir(fullfile(myDataPath.output, 'derivatives', 'age'));
+if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+    mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
 end
 
-figureName = fullfile(myDataPath.output, 'derivatives', 'age', 'SupFigS1_corrAgeVslatency_8mA');
+figureName = fullfile(myDataPath.output, 'derivatives', 'images', 'SupFigS1_corrAgeVslatency_8mA');
 set(gcf, 'PaperPositionMode', 'auto')
 print('-dpng', '-r300', figureName)
 print('-depsc', '-r300', figureName)

diff --git a/scripts/makeSupFig2to5_responses.m b/scripts/makeSupFig2to5_responses.m
@@ -94,8 +94,8 @@
         out{iRow, iCol}.subjectsN1Values = subjectsN1Values;
 
         % calculate and store the r and p for the age vs variance in latency
-        [varlat_r, varlat_p] = corr(subjectsN1Values(~isnan(subjectsN1Values(:, 1)) & ~isnan(subjectsN1Values(:, 3)), 1), ...
-                                    subjectsN1Values(~isnan(subjectsN1Values(:, 1)) & ~isnan(subjectsN1Values(:, 3)), 3), 'Type', 'Spearman');
+        [varlat_r, varlat_p] = corr(subjectsN1Values(~isnan(subjectsN1Values(:, 1)) & ~isnan(subjectsN1Values(:, 4)), 1), ...
+                                    subjectsN1Values(~isnan(subjectsN1Values(:, 1)) & ~isnan(subjectsN1Values(:, 4)), 4), 'Type', 'Spearman');
         out{iRow, iCol}.varlat_r = varlat_r;
         out{iRow, iCol}.varlat_p = varlat_p;
         all_varlat_p(end + 1, :) = [iRow, iCol, varlat_p];
@@ -178,15 +178,17 @@
     end
 end
 
-
-figureName = fullfile(myDataPath.output, 'derivatives', 'age', 'SupFigS2_AgeVsRatioN1s');
+% save
+if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+    mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
+end
+figureName = fullfile(myDataPath.output, 'derivatives', 'images', 'SupFigS2_AgeVsRatioN1s');
 set(gcf,'PaperPositionMode', 'auto')
 print('-dpng', '-r300', figureName)
 print('-depsc', '-r300', figureName)
 
 
 
-
 %% 
 %  Generate supplementary figure 3 that displays the variance in latencies for each of the connections between the end-point areas
 
@@ -198,27 +200,31 @@
 
         % age vs variance latencies
         subplot(size(conn_matrix, 1), size(conn_matrix, 2), outInd);    hold on;
-        plot(subjectsN1Values(:, 1), 1000 * subjectsN1Values(:, 3), 'k.', 'MarkerSize', 10);
+        plot(subjectsN1Values(:, 1), subjectsN1Values(:, 4), 'k.', 'MarkerSize', 10);
 
         % determine the number of samples
         n = sum(~isnan(subjectsN1Values(:, 3)));
 
         %
         title(strrep(out{iRow, iCol}.name, '_', '\_'));
-        xlim([0 60]); ylim([0 1]);
+        xlim([0 60]);
+        ylim([0 (max(subjectsN1Values(:, 4)))])
         if iRow == size(conn_matrix, 1),    xlabel('Age (years)'); end
         if iCol == 1,                       ylabel('Varience in N1 latency (ms)'); end
 
         %
-        text(40, 0.9, ['\rho=', num2str(round(out{iRow, iCol}.varlat_r, 2)), ' (n=', num2str(n, 2), ')']);
-        text(40, 0.8, ['P_f_d_r=', num2str(round(out{iRow, iCol}.varlat_p_fdr, 2))]);
+        text(40, max(subjectsN1Values(:, 4)) * .9, ['\rho=', num2str(round(out{iRow, iCol}.varlat_r, 2)), ' (n=', num2str(n, 2), ')']);
+        text(40, max(subjectsN1Values(:, 4)) * .8, ['P_f_d_r=', num2str(round(out{iRow, iCol}.varlat_p_fdr, 2))]);
 
         hold off;
     end
 end
 
-
-figureName = fullfile(myDataPath.output, 'derivatives', 'age', 'SupFigS3_AgeVsLatVar_N1');
+% save
+if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+    mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
+end
+figureName = fullfile(myDataPath.output, 'derivatives', 'images', 'SupFigS3_AgeVsLatVar_N1');
 set(gcf,'PaperPositionMode', 'auto')
 print('-dpng', '-r300', figureName)
 print('-depsc', '-r300', figureName)
@@ -273,7 +279,11 @@
 end
 set(gca, 'XTick', 20:20:100)
 
-figureName = fullfile(myDataPath.output, 'derivatives', 'age', 'SupFigS4_MeanVsVariance_N1');
+% save
+if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+    mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
+end
+figureName = fullfile(myDataPath.output, 'derivatives', 'images', 'SupFigS4_MeanVsVariance_N1');
 set(gcf,'PaperPositionMode', 'auto');
 print('-dpng', '-r300', figureName);
 print('-depsc', '-r300', figureName);
@@ -328,12 +338,17 @@
     end
 end
 
-figureName = fullfile(myDataPath.output, 'derivatives', 'age', 'SupFigS5_MeanVsFWHM');
+% save
+if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+    mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
+end
+figureName = fullfile(myDataPath.output, 'derivatives', 'images', 'SupFigS5_MeanVsFWHM');
 set(gcf,'PaperPositionMode', 'auto');
 print('-dpng', '-r300', figureName);
 print('-depsc', '-r300', figureName);
 
 
+
 % 
 % 
 % 

diff --git a/scripts/makeSupFig6and7_exploreSOZ.m b/scripts/makeSupFig6and7_exploreSOZ.m
@@ -209,6 +209,10 @@
 [~, ~, ~, p_vals_resp_FDR]  = fdr_bh([n1Latencies(p_indices_resp).respSOZ_p], 0.05, 'pdep');
 [~, ~, ~, p_vals_stim_FDR]  = fdr_bh([n1Latencies(p_indices_stim).stimSOZ_p], 0.05, 'pdep');
 
+% print the FDR correct p-values
+disp(['Response SOZvsNon-SOZ corrected p-values: ', char(strjoin(string(p_vals_resp_FDR), ', '))]);
+disp(['Stim SOZvsNon-SOZ corrected p-values: ', char(strjoin(string(p_vals_stim_FDR), ', '))]);
+
 % put FDR p-values back into the table
 for respIdx = 1:length(p_indices_resp)
     n1Latencies(p_indices_resp(respIdx)).respSOZ_pFDR = p_vals_resp_FDR(respIdx);
@@ -339,7 +343,11 @@
 lgd.FontSize = 20;
 set(gcf,'color', 'w');
 
-figureName = fullfile(myDataPath.output, 'derivatives', 'age', 'SupFigS6_LatencyRespSOZ');
+% save
+if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+    mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
+end
+figureName = fullfile(myDataPath.output, 'derivatives', 'images', 'SupFigS6_LatencyRespSOZ');
 set(gcf, 'renderer', 'Painters')
 set(gcf,'PaperPositionMode', 'auto')
 print('-dpng', '-r300', figureName)
@@ -424,7 +432,11 @@
 lgd.FontSize = 20;
 set(gcf,'color', 'w');
 
-figureName = fullfile(myDataPath.output, 'derivatives', 'age', 'SupFigS7_LatencyStimSOZ');
+% save
+if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+    mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
+end
+figureName = fullfile(myDataPath.output, 'derivatives', 'images', 'SupFigS7_LatencyStimSOZ');
 set(gcf, 'renderer', 'Painters')
 set(gcf, 'PaperPositionMode', 'auto')
 print('-dpng', '-r300', figureName)

diff --git a/scripts/makeSupFig8_volumeConduction.m b/scripts/makeSupFig8_volumeConduction.m
@@ -82,10 +82,12 @@
 xlabel('Standard deviation (ms)')
 ylabel('Number of stimulation pairs')
 
-figureName = fullfile(myDataPath.output, 'derivatives', 'age', 'SupFigS8_volumeConductionCheck');
+% save
+if ~exist(fullfile(myDataPath.output, 'derivatives', 'images'), 'dir')
+    mkdir(fullfile(myDataPath.output, 'derivatives', 'images'));
+end
+figureName = fullfile(myDataPath.output, 'derivatives', 'images', 'SupFigS8_volumeConductionCheck');
 set(gcf, 'PaperPositionMode', 'auto')
 print('-dpng', '-r300', '-painters', figureName)
 print('-depsc2', '-r300', '-painters', figureName)
 
-
-