scripts/Figure_3_and_4.m

%% Plot Figure 3 and 4: Step 3: Plot Time-Frequnecy Results and tf-ROIs bar plots and Correlation Analysis
clear; clc; close all;

cwd = pwd; 
addpath(cwd);

datalocation = [cwd '\ALL_DATA\ALL_Processed_Data\'];   % Data are here

% cd(datalocation);



% % sort all subject groups

[~, ~, groupTable] = xlsread([ cwd '\Patients_MS.xlsx'],'ALL_GROUP');

groupIDs = cell2mat(groupTable(2:end,:) );



% % load clinical scores for correlation analysis

[~, ~, groupInfo] = xlsread([ cwd '\Patients_MS.xlsx'],'Ped_Subjs');



CTLids    = groupIDs(:,1); CTLids   (isnan(CTLids))    = [];

PD_NFZids = groupIDs(:,2); PD_NFZids(isnan(PD_NFZids)) = [];

PD_FZids  = groupIDs(:,3); PD_FZids(isnan(PD_FZids))   = [];

clear groupIDs



% % Import all analysis results here to plot

%  #################### CONTROLS #####################################

for n = 1:length(CTLids)

    

    disp([datalocation,'Control',num2str(CTLids(n)),'_ANALYZED.mat']);

    load([datalocation,'Control',num2str(CTLids(n)),'_ANALYZED.mat']);    

 

    CTL.POWER(n,:,:,:,:)   = MainOuts.POWER;

    clear MainOuts

end



% % #################### PD NON-FREEZERS #############################

for n = 1:length(PD_NFZids)

    disp([datalocation,'PD',num2str(PD_NFZids(n)),'_ANALYZED.mat']);

    load([datalocation,'PD',num2str(PD_NFZids(n)),'_ANALYZED.mat']);    

    

    NFZ.POWER(n,:,:,:,:)   = MainOuts.POWER;

    clear MainOuts 

end



% % #################### PD FREEZERS #################################

for n = 1:length(PD_FZids)

    disp([datalocation,'PD',num2str(PD_FZids(n)),'_ANALYZED.mat']);

    load([datalocation,'PD',num2str(PD_FZids(n)),'_ANALYZED.mat']);    

    

    FZ.POWER(n,:,:,:,:)   = MainOuts.POWER;

    clear MainOuts

end





%% Time-FREQUENCY POWER

tx2disp=-500:2:2000;

XLIM = [-500 2000];



min_freq = 1.0233;    max_freq = 50;    num_freqs=50;

frex = logspace(log10(min_freq),log10(max_freq),num_freqs); 



CONDI = 1; % 1=GO cue;

CHANI(1)   = find(strcmpi('Cz',{chanlocs.labels}));



% % %%%%%% POWER

% % % POWER Statistics: NFZ-CTL and FZ-CTL

YLIM = [1 50];





figure('rend','painters','pos',[10 10 1000 600])

ch=1;

CTLPOWER = CTL.POWER(:,CHANI(ch),:,:,CONDI);  

NFZPOWER = NFZ.POWER(:,CHANI(ch),:,:,CONDI);  

FZPOWER  = FZ. POWER(:,CHANI(ch),:,:,CONDI);



%%%% TF plots

clim = [-6 6];

subplot(2,3,1); imagesc(tx2disp,[], squeeze(mean(CTLPOWER,1)) ); axis xy; hold on; colormap jet; 

plot([0 0],YLIM,'k:'); title('Controls (CTL)'); set(gca,'xlim',XLIM,'ylim',YLIM,'clim',clim,'YTick',1:4:length(frex),'YTickLabel',round(frex(1:4:end))); colorbar



subplot(2,3,2); imagesc(tx2disp,[], squeeze(mean(NFZPOWER,1)) ); axis xy; hold on; colormap jet; 

plot([0 0],YLIM,'k:'); title('PDFOG- (NFZ)'); set(gca,'xlim',XLIM,'ylim',YLIM,'clim',clim,'YTick',1:4:length(frex),'YTickLabel',round(frex(1:4:end)));colorbar



subplot(2,3,3); imagesc(tx2disp,[], squeeze(mean(FZPOWER,1)) ); axis xy; hold on; colormap jet; 

plot([0 0],YLIM,'k:'); title('PDFOG+ (FZ)'); set(gca,'xlim',XLIM,'ylim',YLIM,'clim',clim,'YTick',1:4:length(frex),'YTickLabel',round(frex(1:4:end)));colorbar



%%%% TF with ttest2: runthreshold2 

clim = [-3 3];

subplot(2,3,4); imagesc(tx2disp,[], squeeze(mean(NFZPOWER,1)) - squeeze(mean(CTLPOWER,1)) ); axis xy; hold on; colormap jet; 

[Corrected_P] = Run_Thresh_2D_AS(squeeze(NFZPOWER) , squeeze(CTLPOWER),'between');

contour(tx2disp,1:50,Corrected_P,'k','linewidth',2); clear thresh ; plot([0 0],YLIM,'k:'); title('NFZ-CTL'); set(gca,'xlim',XLIM,'ylim',YLIM,'clim',clim,'YTick',1:4:length(frex),'YTickLabel',round(frex(1:4:end))); colorbar

clear Corrected_P



subplot(2,3,5); imagesc(tx2disp,[], squeeze(mean(FZPOWER,1)) - squeeze(mean(CTLPOWER,1)) ); axis xy; hold on; colormap jet; 

[Corrected_P] = Run_Thresh_2D_AS( squeeze(FZPOWER) , squeeze(CTLPOWER),'between');

contour(tx2disp,1:50,Corrected_P,'k','linewidth',2); clear thresh ; plot([0 0],YLIM,'k:'); title('FZ-CTL');set(gca,'xlim',XLIM,'ylim',YLIM,'clim',clim,'YTick',1:4:length(frex),'YTickLabel',round(frex(1:4:end)));colorbar

clear Corrected_P



subplot(2,3,6); imagesc(tx2disp,[], squeeze(mean(FZPOWER,1)) - squeeze(mean(NFZPOWER,1)) ); axis xy; hold on; colormap jet; 

[Corrected_P] = Run_Thresh_2D_AS( squeeze(FZPOWER) , squeeze(NFZPOWER),'between');

contour(tx2disp,1:50,Corrected_P,'k','linewidth',2); clear thresh ; plot([0 0],YLIM,'k:'); title('FZ-NFZ');set(gca,'xlim',XLIM,'ylim',YLIM,'clim',clim,'YTick',1:4:length(frex),'YTickLabel',round(frex(1:4:end)));colorbar

clear Corrected_P



clear CTLPOWER NFZPOWER FZPOWER



suptitle ('Figure 3A and 3B : Cz: GoCue-locked POWER Difference');



%% % Save power values for frequency bands values for correlation analysis

ExpPOWER.CTL{ch} = CTL.POWER(:,CHANI(ch),:,:,CONDI);

ExpPOWER.NFZ{ch} = NFZ.POWER(:,CHANI(ch),:,:,CONDI);

ExpPOWER.FZ{ch}  = FZ. POWER(:,CHANI(ch),:,:,CONDI);



ExpPOWER.groups  = groupTable;

% % save POW_CTLNFZFZ_Subjs.mat ExpPOWER % save for correlation analysis



% % %%%% Define: Delta and Beta for pedaling Initiation

SubjIDs = cell2mat(ExpPOWER.groups(2:end,:) );

ch = 1;



% Theta Frequnecy band: pedaling Initiation

fqidx1 = max(find(frex <=3.5) ) ;   fqidx2 =  max(find(frex <=7.5) );

tmidx1 = find(round(tx2disp)==0); tmidx2 = find(round(tx2disp)==400);



% Beta Frequnecy band: pedaling execution

fqidx3 = max(find(frex <=12.5) );   fqidx4 =  max(find(frex <=30) );

tmidx3 = find(round(tx2disp)==400); tmidx4 = find(round(tx2disp)==2000);



% pedaling Initiation (0-400 ms)

powCTL_GI.Te(:,ch) = squeeze(mean(mean(ExpPOWER.CTL{ch}(:,:,fqidx1:fqidx2,tmidx1:tmidx2),3),4 ));  powCTL_GI.Be(:,ch) = squeeze(mean(mean(ExpPOWER.CTL{ch}(:,:,fqidx3:fqidx4,tmidx1:tmidx2),3),4 ));

powNFZ_GI.Te(:,ch) = squeeze(mean(mean(ExpPOWER.NFZ{ch}(:,:,fqidx1:fqidx2,tmidx1:tmidx2),3),4 ));  powNFZ_GI.Be(:,ch) = squeeze(mean(mean(ExpPOWER.NFZ{ch}(:,:,fqidx3:fqidx4,tmidx1:tmidx2),3),4 ));

powFZ_GI.Te(:,ch)  = squeeze(mean(mean(ExpPOWER.FZ{ch} (:,:,fqidx1:fqidx2,tmidx1:tmidx2),3),4 ));  powFZ_GI.Be(:,ch)  = squeeze(mean(mean(ExpPOWER.FZ{ch} (:,:,fqidx3:fqidx4,tmidx1:tmidx2),3),4 ));



powCTL_GI.Te(:,2) = SubjIDs(:,1);   powCTL_GI.Be(:,2) = SubjIDs(:,1); 

powNFZ_GI.Te(:,2) = SubjIDs(:,2);   powNFZ_GI.Be(:,2) = SubjIDs(:,2);

powFZ_GI.Te(:,2) =  SubjIDs(:,3);   powFZ_GI.Be(:,2) =  SubjIDs(:,3); 



%%% pedaling (0-2000 ms)

powCTL_ped.Te(:,ch) = squeeze(mean(mean(ExpPOWER.CTL{ch}(:,:,fqidx1:fqidx2,tmidx1:tmidx4),3),4 ));  powCTL_ped.Be(:,ch) = squeeze(mean(mean(ExpPOWER.CTL{ch}(:,:,fqidx3:fqidx4,tmidx1:tmidx4),3),4 ));

powNFZ_ped.Te(:,ch) = squeeze(mean(mean(ExpPOWER.NFZ{ch}(:,:,fqidx1:fqidx2,tmidx1:tmidx4),3),4 ));  powNFZ_ped.Be(:,ch) = squeeze(mean(mean(ExpPOWER.NFZ{ch}(:,:,fqidx3:fqidx4,tmidx1:tmidx4),3),4 ));

powFZ_ped.Te(:,ch)  = squeeze(mean(mean(ExpPOWER.FZ{ch} (:,:,fqidx1:fqidx2,tmidx1:tmidx4),3),4 ));  powFZ_ped.Be(:,ch)  = squeeze(mean(mean(ExpPOWER.FZ{ch} (:,:,fqidx3:fqidx4,tmidx1:tmidx4),3),4 ));



powCTL_ped.Te(:,2) = SubjIDs(:,1);   powCTL_ped.Be(:,2) = SubjIDs(:,1); 

powNFZ_ped.Te(:,2) = SubjIDs(:,2);   powNFZ_ped.Be(:,2) = SubjIDs(:,2);

powFZ_ped.Te(:,2)  = SubjIDs(:,3);   powFZ_ped.Be(:,2)  = SubjIDs(:,3); 



% % Topo plots

figure('rend','painters','pos',[10 10 800 500])

pvl = 0.01;



[~,P,~,~]= ttest2( mean(mean(FZ.POWER(:,:,fqidx1:fqidx2,tmidx1:tmidx2,CONDI,1),3),4), mean(mean(CTL.POWER(:,:,fqidx1:fqidx2,tmidx1:tmidx2,CONDI,1),3),4)  ); 

P(P>=pvl)=NaN; P(P<pvl)=1; P(isnan(P))=0; 

subplot(221); topoplot( mean(mean(squeeze(mean(FZ.POWER(:,:,fqidx1:fqidx2,tmidx1:tmidx2,CONDI),1 )),2),3) - mean(mean(squeeze(mean(CTL.POWER(:,:,fqidx1:fqidx2,tmidx1:tmidx2,CONDI),1 )),2),3),...

    chanlocs,'maplimits',[-4 4],'electrodes','on','emarker2', {find(P),'d','k',5,1});    title('Theta; PDFOG+ - Controls'); clear P; colormap jet; 



[~,P,~,~]= ttest2( mean(mean(FZ.POWER(:,:,fqidx1:fqidx2,tmidx1:tmidx2,CONDI,1),3),4), mean(mean(NFZ.POWER(:,:,fqidx1:fqidx2,tmidx1:tmidx2,CONDI,1),3),4)  ); 

P(P>=pvl)=NaN; P(P<pvl)=1; P(isnan(P))=0; 

subplot(222); topoplot( mean(mean(squeeze(mean(FZ.POWER(:,:,fqidx1:fqidx2,tmidx1:tmidx2,CONDI),1 )),2),3) - mean(mean(squeeze(mean(NFZ.POWER(:,:,fqidx1:fqidx2,tmidx1:tmidx2,CONDI),1 )),2),3),...

    chanlocs,'maplimits',[-4 4],'electrodes','on','emarker2', {find(P),'d','k',5,1});    title('Theta; PDFOG+ - PDFOG-'); clear P; colormap jet; 



[~,P,~,~]= ttest2( mean(mean(FZ.POWER(:,:,fqidx3:fqidx4,tmidx1:tmidx2,CONDI,1),3),4), mean(mean(CTL.POWER(:,:,fqidx3:fqidx4,tmidx1:tmidx2,CONDI,1),3),4)  ); 

P(P>=pvl)=NaN; P(P<pvl)=1; P(isnan(P))=0;  

subplot(223); topoplot( mean(mean(squeeze(mean(FZ.POWER(:,:,fqidx3:fqidx4,tmidx1:tmidx2,CONDI),1 )),2),3) - mean(mean(squeeze(mean(CTL.POWER(:,:,fqidx3:fqidx4,tmidx1:tmidx2,CONDI),1 )),2),3),...

    chanlocs,'maplimits',[-1 1],'electrodes','on','emarker2', {find(P),'d','k',5,1});    title('Beta; PDFOG+ - Controls'); clear P; colormap jet; 



[~,P,~,~]= ttest2( mean(mean(FZ.POWER(:,:,fqidx3:fqidx4,tmidx1:tmidx2,CONDI,1),3),4), mean(mean(NFZ.POWER(:,:,fqidx3:fqidx4,tmidx1:tmidx2,CONDI,1),3),4)  ); 

P(P>=pvl)=NaN; P(P<pvl)=1; P(isnan(P))=0;  

subplot(224); topoplot( mean(mean(squeeze(mean(FZ.POWER(:,:,fqidx3:fqidx4,tmidx1:tmidx2,CONDI),1 )),2),3) - mean(mean(squeeze(mean(NFZ.POWER(:,:,fqidx3:fqidx4,tmidx1:tmidx2,CONDI),1 )),2),3),...

    chanlocs,'maplimits',[-1 1],'electrodes','on','emarker2', {find(P),'d','k',5,1});    title('Beta; PDFOG+ - PDFOG-'); clear P; colormap jet; 



suptitle('Figure 3E and 3F : Topo plots (Theta and beta power; 0-400 ms time window)'); 



%% % Plot selcted band for boxplot with scatter plot to see each values

%%%% for pedaling ROIs

ThetabandBox1Ped = [powCTL_ped.Te(:,1); powNFZ_ped.Te(:,1); powFZ_ped.Te(:,1) ];

BetabandBox2Ped = [powCTL_ped.Be(:,1); powNFZ_ped.Be(:,1); powFZ_ped.Be(:,1) ];



%%%% group data

nCTL = length(powCTL_ped.Te(:,1));

nNFZ = length(powNFZ_ped.Te(:,1));

nFZ  = length(powFZ_ped.Te(:,1));



for nn = 1:nCTL

    bandMdVar1{nn,1} = sprintf('%s', 'CTL');    
    bandMdVar1{nn,2} =1 ; 
end 
for nn = nCTL+1: nNFZ+ nNFZ
    bandMdVar1{nn,1} = sprintf('%s', 'NFZ');  
    bandMdVar1{nn,2}=2; 
end

for nn = nCTL+nNFZ+1:nCTL+nNFZ+nFZ
    bandMdVar1{nn,1} = sprintf('%s', 'FZ');  
    bandMdVar1{nn,2}=3; 
end

figure('rend','painters','pos',[10 10 800 900]);

%%%%% for Pedaling Initiation tf-ROIs
ThetabandBox1GI = [powCTL_GI.Te(:,1); powNFZ_GI.Te(:,1); powFZ_GI.Te(:,1) ];
BetabandBox2GI = [powCTL_GI.Be(:,1); powNFZ_GI.Be(:,1); powFZ_GI.Be(:,1) ];

subplot(221);
boxplot(ThetabandBox1GI,bandMdVar1(:,1), 'OutlierSize',12);  hold on;
gscatter( cell2mat(bandMdVar1(:,2)) , ThetabandBox1GI, bandMdVar1(:,1), 'kgr'); hold off; ylabel('POWER (dB)'); title('0-400 ms: Theta power'); ylim([-2 6]);

subplot(222);
boxplot(BetabandBox2GI,bandMdVar1(:,1), 'OutlierSize',12);  hold on;
gscatter( cell2mat(bandMdVar1(:,2)) , BetabandBox2GI, bandMdVar1(:,1), 'kgr'); hold off; ylabel('POWER (dB)'); title('0-400 ms: Beta power');ylim([-6 3]);

%%%%% for Pedaling Execuation tf-ROIs
subplot(223);
boxplot(ThetabandBox1Ped,bandMdVar1(:,1), 'OutlierSize',12);  hold on;
gscatter( cell2mat(bandMdVar1(:,2)) , ThetabandBox1Ped, bandMdVar1(:,1), 'kgr'); hold off; ylabel('POWER (dB)'); title('0-2000 ms: Theta power'); ylim([-2 6]);

subplot(224);
boxplot(BetabandBox2Ped,bandMdVar1(:,1), 'OutlierSize',12);  hold on;
gscatter( cell2mat(bandMdVar1(:,2)) , BetabandBox2Ped, bandMdVar1(:,1), 'kgr'); hold off; ylabel('POWER (dB)'); title('0-2000 ms: Beta power'); ylim([-6 3]);

suptitle('Figure 3C and 3D : Theta and Beta tf-ROI power');

%% ############################################################ Figure 4 ###############################################
% % Correlation Analysis with Power values

groupIDs = cell2mat(groupInfo(2:end,2:end) );

idx1 = find(groupIDs(:,1)==1); idx2 = find(groupIDs(:,1)==2); idx3 = find(groupIDs(:,1)==3);
CTLids = groupIDs(idx1,:);
NFZids = groupIDs(idx2,:);
FZids  = groupIDs(idx3,:);

MOCA = groupIDs([idx2; idx3],3);
FOG  = groupIDs([idx2; idx3],4);
UPDRS  = groupIDs([idx2; idx3],5);

Clinical_Score = [MOCA FOG UPDRS];
% % % correlation Type
corrType = 'Spearman';

% % % Correlation Analysis: Organize all Data

%%%% for pedaling Initiation: 0-400 ms
Thetadata = [powNFZ_GI.Te(:,1); powFZ_GI.Te(:,1) ];
Betadata =  [powNFZ_GI.Be(:,1); powFZ_GI.Be(:,1) ];

POWER_BANDS = [Thetadata Betadata]; 

for var = 1:2
    figure('rend','painters','pos',[10 10 400 900]);
    % with FOG scores
    subplot(311); SS = plot( FOG, POWER_BANDS(:,var), 'k+');hold on;  
    [R,P] = corr( FOG, POWER_BANDS(:,var),'type',corrType);  set(SS, 'MarkerSize', 8, 'LineWidth', 2);   l = lsline ; set(l,'LineWidth', 2); hold off;
    xlabel('FOG Score', 'FontSize', 10); set(gca, 'FontSize', 10, 'YMinorTick','on','XMinorTick','on'); 
    title(['\color{black} rho=' num2str(R,'%3.2f'),';  P=' num2str(P,'%3.3f')]); clear SS R P l; xlim([min(FOG)-1 max(FOG)+1]); 

    % with UPDRS III
    subplot(312); SS = plot( UPDRS, POWER_BANDS(:,var), 'k+');hold on;  
    [R,P] = corr( UPDRS, POWER_BANDS(:,var),'type',corrType);  set(SS, 'MarkerSize', 8, 'LineWidth', 2);   l = lsline ; set(l,'LineWidth', 2); hold off;
    xlabel('UPDRS Score', 'FontSize', 10);  set(gca, 'FontSize', 10, 'YMinorTick','on','XMinorTick','on'); 
    title(['\color{black} rho=' num2str(R,'%3.2f'),';  P=' num2str(P,'%3.3f')]); clear SS R P l; xlim([min(UPDRS)-1 max(UPDRS)+1]);
    
    % with MOCA
    subplot(313); SS = plot( MOCA, POWER_BANDS(:,var), 'k+');hold on;  
    [R,P] = corr( MOCA, POWER_BANDS(:,var),'type',corrType);  set(SS, 'MarkerSize', 8, 'LineWidth', 2);   l = lsline ; set(l,'LineWidth', 2); hold off;
    xlabel('MOCA Score', 'FontSize', 10);  set(gca, 'FontSize', 10, 'YMinorTick','on','XMinorTick','on'); 
    title(['\color{black} rho=' num2str(R,'%3.2f'),';  P=' num2str(P,'%3.3f')]); clear SS R P l; xlim([min(MOCA)-1 max(MOCA)+1]); 

    if var ==1
        suptitle('Figure 4A: Correlation against Theta band values')
    elseif var ==2
        suptitle('Figure 4B: Correlation against Beta band values')
    end
    
end