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ERP_byTarget_Plots_Stats.m
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ERP_byTarget_Plots_Stats.m
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% /////////////////////////////////////////////////////////////////////////
%% Load settings
load('filt_byTargets_v4_Settings.mat'); %setting for target-aligned trials
% /////////////////////////////////////////////////////////////////////////
%% Location of saved ERP results
saveLocation = [exp.dataLocation '\ProcessData\']; % set save directory of data set
% /////////////////////////////////////////////////////////////////////////
%% Location to save figures
saveFig = [pwd '\Figures\ERP\']; % set save directory of data set
% if folder doesn't exist yet, create one
if ~exist(saveFig)
mkdir(saveFig);
end
% /////////////////////////////////////////////////////////////////////////
%% ------------------ Load Previously Saved Data --------------------------
% /////////////////////////////////////////////////////////////////////////
% Load data from ERP_byTarget.m
load([saveLocation 'erp_out_byTarget.mat'])
% Load data from Anal_ERP_Orient_byCatchTrial.m
erp_catchtrials = cell2mat(struct2cell(load([saveLocation 'erp_out_catch_trials.mat'],'erp_out')));
% -------------------------------------------------------------------------
% +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
% -------------------------------------------------------------------------
%% Select electrodes for analysis
% List electrodes with EOGs if want to check EOGs
% elect_erp = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34];
% el_erp_names = {'M2';'Oz';'Pz';'Cz';'FCz';'Fz';'O1';'O2';'PO3';'PO4';'P7';'P8';'P5';'P6';'P3';'P4';'CP5';...
% 'CP6';'CP1';'CP2';'C3';'C4';'FC5';'FC6';'FC1';'FC2';'F7';'F8';'F3';'F4';'Fp1';'Fp2';'VEOG';'HEOG'};
% List electrodes to get ERPs and topograph plots
elect_erp = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32];
el_erp_names = {'M2';'Oz';'Pz';'Cz';'FCz';'Fz';'O1';'O2';'PO3';'PO4';'P7';'P8';'P5';'P6';'P3';'P4';'CP5';...
'CP6';'CP1';'CP2';'C3';'C4';'FC5';'FC6';'FC1';'FC2';'F7';'F8';'F3';'F4';'Fp1';'Fp2'};
% :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
%% :::::::::::::::::: Plot the ERPs by electrode ::::::::::::::::::::::::
% ::::::::::::::::::: Subtract Catch Trial ::::::::::::::::::::::::
% :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
% -------------------------------------------------------------------------
% Average across subjects by errors
erp_out_byerr2(:,:,1) = squeeze((mean(erp_out_x(:,:,:),1)-mean(erp_catchtrials(:,:,:),1))); %small errors
erp_out_byerr2(:,:,2) = squeeze((mean(erp_out_n(:,:,:),1)-mean(erp_catchtrials(:,:,:),1))); %large errors
% Average across subjects - catch trials
erp_out_bycatch(:,:) = squeeze(mean(erp_catchtrials(:,:,:),1));
% -------------------------------------------------------------------------
% Plot ERPs with error bars
for ii = 1:length(elect_erp)
i_elect = elect_erp(ii); %for doing only a selection of electrodes
% i_elect = ii; %if want to select one making ERPs
% get axes limits
xmin = -200; xmax = 800;
ymin = -6; ymax = 6; %brain electrodes
% ymin = -5; ymax = 30; %VEOG: ii=33
% ymin = -2; ymax = 4; %HEOG: ii=34
figure('Color',[1 1 1]);
boundedline(erp_time,erp_out_byerr2(i_elect,:,1),...
squeeze(std((erp_out_x(:,i_elect,:)-erp_catchtrials(:,i_elect,:)),[],1))./sqrt(length(exp.participants)),'c',...
erp_time,erp_out_byerr2(i_elect,:,2),...
squeeze(std((erp_out_n(:,i_elect,:)-erp_catchtrials(:,i_elect,:)),[],1))./sqrt(length(exp.participants)),'m');
hold on
line([xmin xmax],[0 0],'color','k','LineWidth',1.5) %horizontal line
line([0 0],[ymin ymax],'color','k','LineWidth',1.5) %vertical line
% line([50 50],[ymin ymax],'LineStyle',':','LineWidth',1.5) %vertical line for mask onset
line([567 567],[ymin ymax],'color','r','LineStyle','--','LineWidth',1.5) %vertical line for color wheel onset
set(gca,'ydir','reverse'); xlim([xmin xmax]); ylim([ymin ymax])
title([el_erp_names{ii} ': ERPs by Response Error']);
xlabel('Time (ms)'); ylabel('Voltage (uV)');
xticks(-200:100:xmax);
yticks(ymin:2:ymax)
% grid on
legend({'Accurate','Guess'},'Location','best');
savefig([saveFig 'ERP-NoT_' el_erp_names{ii}])
end
clear ii xmax xmin ymin ymax
% -------------------------------------------------------------------------
% /////////////////////////////////////////////////////////////////////////
% '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
%% ''''''''''''''''''''''' Topographys '''''''''''''''''''''''''''''
% '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
% /////////////////////////////////////////////////////////////////////////
% List electrodes to get topograph plots
elect_erp = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32];
% el_erp_names = {'M2';'Oz';'Pz';'Cz';'FCz';'Fz';'O1';'O2';'PO3';'PO4';'P7';'P8';'P5';'P6';'P3';'P4';'CP5';...
% 'CP6';'CP1';'CP2';'C3';'C4';'FC5';'FC6';'FC1';'FC2';'F7';'F8';'F3';'F4';'Fp1';'Fp2'};
% Difference topplots ----------------------------------------------------------------------------
% average across subjects by errors
erp_out_byerr(:,:,1) = squeeze(mean((erp_out_x(:,:,:)-erp_catchtrials(:,:,:)),1)); %small errors
erp_out_byerr(:,:,2) = squeeze(mean((erp_out_n(:,:,:)-erp_catchtrials(:,:,:)),1)); %large errors
erp_out_diff(:,:,1) = erp_out_byerr(:,:,1) - erp_out_byerr(:,:,2); %small-large
% average across subjects - catch trials
erp_out_bycatch(:,:) = squeeze(mean(erp_catchtrials(:,:,:),1));
clear erp_out_byerr
% ------------------------------------------------------------------------------------------------
% Set the range of time to consider
tWin{1} = [80 140]; %P1
tWin{2} = [140 200]; %N1
tWin{3} = [200 255]; %P2
tWin{4} = [255 360]; %N2
tWin{5} = [360 500]; %P3
CLims1 = [-3 3]; %range in microvolts
nconds = 1; %number of plots
for tw_i = 1:length(tWin) %loop through several time windows
itWin = tWin{tw_i}; %select each time range if looping
%this code finds the times you want from the times variable
time_window = find(erp_time>= itWin(1),1):find(erp_time>= itWin(2),1)-1;
figure('Color',[1 1 1]); %set-up figure
%loop through conditions to make plot of each
for i_cond = 1:nconds
set(gca,'Color',[1 1 1]);
temp = mean(erp_out_diff(:,time_window,i_cond),2)'; %ERP within time window
temp(1) = NaN; %so M2 is not included
topoplot(temp,chan_locs,'whitebk','on','plotrad',0.6,'maplimits',CLims1,...
'plotchans',elect_erp,'emarker',{'.','k',11,1})
title('Accurate-Guess');
t = colorbar('peer',gca);
set(get(t,'ylabel'),'String', 'Voltage (uV)');
clear temp
end
% Overall subplot title
supertitle([num2str(itWin(1)) ' to ' num2str(itWin(2)) ' ms'],...
'FontSize',10.5)
savefig([saveFig 'ERP-NoT_Topo_' num2str(itWin(1)) ' to ' num2str(itWin(2)) ' ms'])
clear itWin time_window i_cond
end
clear tw_i nconds conds tWin CLims CLims1 t time1 time2 i_elect
clear erp_out_diff
% -------------------------------------------------------------------------
% /////////////////////////////////////////////////////////////////////////
%% ::::::::::::::::::::: Permutation Test :::::::::::::::::::::::::::::::
% \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
% -------------------------------------------------------------------------
% **Need code from: https://openwetware.org/wiki/Mass_Univariate_ERP_Toolbox
% -------------------------------------------------------------------------
% Just brain electrodes
elect_erp = [2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32];
el_erp_names = {'Oz';'Pz';'Cz';'FCz';'Fz';'O1';'O2';'PO3';'PO4';'P7';'P8';'P5';'P6';'P3';'P4';'CP5';...
'CP6';'CP1';'CP2';'C3';'C4';'FC5';'FC6';'FC1';'FC2';'F7';'F8';'F3';'F4';'Fp1';'Fp2'};
% -------------------------------------------------------------------------
% ERPs in paper
timewin{1} = [80 140]; %P1
timewin{2} = [140 200]; %N1
timewin{3} = [200 255]; %P2
timewin{4} = [255 360]; %N2
timewin{5} = [360 500]; %P3
% electrode x time points x conditions x subjects array
erp_stat = NaN(length(elect_erp),length(timewin),2,length(exp.participants)); %pre-allocate
for i_time = 1:length(timewin)
timelim = find(erp_time>=timewin{i_time}(1) & erp_time<=timewin{i_time}(2));
for i_part = 1:length(exp.participants)
for ii = 1:length(elect_erp)
i_elect = elect_erp(ii); %for doing only a selection of electrodes
% (participant x electrode x time)
% Subtract out catch trials
erp_stat(i_elect,i_time,1,i_part) = squeeze(mean((erp_out_x(i_part,i_elect,timelim)-erp_catchtrials(i_part,i_elect,timelim)),3)); %small errors
erp_stat(i_elect,i_time,2,i_part) = squeeze(mean((erp_out_n(i_part,i_elect,timelim)-erp_catchtrials(i_part,i_elect,timelim)),3)); %large errors
% Save electrode names
permtest.elect_id{ii,1} = el_erp_names{ii};
end
clear ii i_elect
end
clear i_part timelim
end
clear i_time
% One sample/repeated-measures permutation test
% Open pval for outcome
% data(Channel x Time x Participant)
[pval, t_orig, tmx_ptile] = mxt_perm1(squeeze(erp_stat(2:32,:,1,:)-erp_stat(2:32,:,2,:)),1e5);
writematrix(pval,'ERP_permtest_pval.txt','Delimiter','tab')
clear pval t_orig tmx_ptile seed_state est_alpha timewin
% +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
% clears variables that end/begin with...
clear -regexp \<permtest_ \<ttest_
clear time_window time1 time2 erp_stat
% +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
% +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
% :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
%% :::::::::::::::::: Plot the ERPs by electrode ::::::::::::::::::::::::
% :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
% +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
% -------------------------------------------------------------------------
% Average across subjects by errors
erp_out_byerr(:,:,1) = squeeze(mean(erp_out_x(:,:,:),1)); %small errors
erp_out_byerr(:,:,2) = squeeze(mean(erp_out_n(:,:,:),1)); %large errors
erp_out_byerr(:,:,3) = squeeze(mean(erp_catchtrials(:,:,:),1)); %catch trials (no target)
% Average across subjects - catch trials
erp_out_bycatch(:,:) = squeeze(mean(erp_catchtrials(:,:,:),1));
% -------------------------------------------------------------------------
% Plot ERPs with error bars
for ii = 1:length(elect_erp)
i_elect = elect_erp(ii); %for doing only a selection of electrodes
% i_elect = ii; %selection done when making ERPs
% get axes limits
xmin = -200; xmax = 800;
ymin = -6; ymax = 10;
% ymin = -5; ymax = 30; %VEOG: ii=33
% ymin = -2; ymax = 4; %HEOG: ii=34
figure('Color',[1 1 1]);
boundedline(erp_time,erp_out_bycatch(i_elect,:),squeeze(std(erp_catchtrials(:,i_elect,:),[],1))./sqrt(length(exp.participants)),'k',...
erp_time,erp_out_byerr(i_elect,:,1),squeeze(std(erp_out_x(:,i_elect,:),[],1))./sqrt(length(exp.participants)),'c',...
erp_time,erp_out_byerr(i_elect,:,2),squeeze(std(erp_out_n(:,i_elect,:),[],1))./sqrt(length(exp.participants)),'m');
hold on
line([xmin xmax],[0 0],'color','k','LineWidth',1.5) %horizontal line
line([0 0],[ymin ymax],'color','k','LineWidth',1.5) %vertical line
% line([50 50],[ymin ymax],'LineStyle',':','LineWidth',1.5) %vertical line for mask onset
line([567 567],[ymin ymax],'color','r','LineStyle','--','LineWidth',1.5) %vertical line for color wheel onset
set(gca,'ydir','reverse'); xlim([xmin xmax]); ylim([ymin ymax])
title([el_erp_names{ii} ': ERPs by Response Error']);
xlabel('Time (ms)'); ylabel('Voltage (uV)');
xticks(-200:100:xmax);
yticks(ymin:2:ymax)
% grid on
legend({'No Target','Accurate','Guess'},'Location','best');
savefig([saveFig 'ERP_' el_erp_names{ii}])
end
clear ii xmax xmin ymin ymax
% -------------------------------------------------------------------------