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sa_contingency_spindles.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Spindle contingencies
% by Til Ole Bergmann 2016
% last modified 2016/11/22 by TOB
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% performs contingency analyses across channels for spindles
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [spindle_contingencies] = sa_contingency_spindles(gcfg, All_spindle_info)
if gcfg.loadPreviousContingencyResults ~= 1 % calculate anew or load existing contingencies?
h1 = figure;
for i = 1:numel(gcfg.subjects) % loop over subjects to generate logidx
contMat{i} = zeros(length(All_spindle_info{i}.eventInfo),length(All_spindle_info{i}.eventInfo)); % setup contingency matrix
logidx{i} = logical(zeros(length(All_spindle_info{i}.eventInfo),length(All_spindle_info{i}.scoring)));
for ch = 1:length(All_spindle_info{i}.eventInfo) % first loop over channels
for e = 1:length(All_spindle_info{i}.eventInfo(ch).startTime) % loop over events
logidx{i}(ch, All_spindle_info{i}.eventInfo(ch).startTime(e):All_spindle_info{i}.eventInfo(ch).endTime(e)) = 1;
end
end % of first loop over channels
for ch = 1:length(All_spindle_info{i}.eventInfo) % second loop over channels to test for condingencies (i.e. overlapping events)
tempContMat{i}{ch} = zeros(length(All_spindle_info{i}.eventInfo(ch).startTime),length(All_spindle_info{i}.eventInfo));
for e = 1:length(All_spindle_info{i}.eventInfo(ch).startTime) % loop over events
tempContMat{i}{ch}(e,:) = sum(logidx{i}(:,All_spindle_info{i}.eventInfo(ch).startTime(e):All_spindle_info{i}.eventInfo(ch).endTime(e)),2) > 0';
end % of loop over events
contMat{i}(ch,:) = mean(tempContMat{i}{ch},1);
end % of second loop over channels
% plot single-subject figures
h2 = figure;
imagesc(contMat{i});
colormap hot;
set(gca,'clim',[0 1]);
colorbar;
set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',10);
set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',10);
set(gca,'yDir','normal');
title({[gcfg.subjectNames{i} ': Spindle contingency matrix']});
ylabel('Given a spindle in channel');
xlabel('there is a spindle in channel');
set(h2, 'Name',[gcfg.subjectNames{i} '_spindle_' gcfg.spindle_timelockevent '_' gcfg.spindle_tsv_flag '_' gcfg.spindle_timelockchannel '_contingencies_' gcfg.timestamp],'NumberTitle','off','units','normalized','outerposition',[0 0 1 1]);
filename = fullfile(gcfg.paths.results, gcfg.subjectNames{i}, [gcfg.subjectNames{i} '_spindle_' gcfg.spindle_timelockevent '_' gcfg.spindle_tsv_flag '_' gcfg.spindle_timelockchannel '_contingencies_' gcfg.timestamp]);
saveas(h2,[filename '.fig']);
set(h2, 'PaperUnits', 'centimeters', 'PaperSize', [33.867 19.05], 'PaperPosition', [0 -1 33.867 19.05]); % [left bottom width height]
print(h2, '-dpdf', '-r300', [filename '.pdf']);
% plot multi-subject figure
figure(h1);
subplot(3,4,i);
imagesc(contMat{i});
colormap hot;
set(gca,'clim',[0 1]);
colorbar;
set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',4);
set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',4);
set(gca,'yDir','normal');
title({[gcfg.subjectNames{i} ': Spindle contingency matrix']});
ylabel('Given a spindle in channel');
xlabel('there is a spindle in channel');
end % of loop over subjects
figure(h1);
set(gcf, 'Name',['All_spindle_' gcfg.spindle_timelockevent '_' gcfg.spindle_tsv_flag '_' gcfg.spindle_timelockchannel '_contingencies_' gcfg.timestamp],'NumberTitle','off','units','normalized','outerposition',[0 0 1 1]);
filename = fullfile(gcfg.paths.results, 'group', ['All_spindle_' gcfg.spindle_timelockevent '_' gcfg.spindle_tsv_flag '_' gcfg.spindle_timelockchannel '_contingencies_' gcfg.timestamp]);
saveas(gcf,[filename '.fig']);
set(gcf, 'PaperUnits', 'centimeters', 'PaperSize', [33.867 19.05], 'PaperPosition', [0 -1 33.867 19.05]); % [left bottom width height]
print(gcf, '-dpdf', '-r300', [filename '.pdf']);
% test against surrogate spindle contingencies %%%%%%%%%%%%%%%%%%%%%%%%
for i = 1:numel(gcfg.subjects) % loop over subjects
tic; % for subjectToc
% first set of loops to create shuffle cell array
for ch = 1:length(All_spindle_info{i}.eventInfo) % loop over channels
% define good epochs (sleepstages) only
goodEpoch.idx = All_spindle_info{i}.scoring(4,:);
goodEpoch.start = find(diff(goodEpoch.idx)>0);
goodEpoch.end = find(diff(goodEpoch.idx)<0);
st = All_spindle_info{i}.eventInfo(ch).startTime'; % start times
et = All_spindle_info{i}.eventInfo(ch).endTime'; % end times
% % plot actual logidx
% dat = [logidx{i}; goodEpoch.idx]; % column 4 is 1 for 'searchstages'
% figure;
% imagesc(dat);
% set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
% set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
for ge = 1:length(goodEpoch.start) % loop over good epochs (GE, ge)
% get distribution of event start and end times for good epoch (sleepstages) only
GE{ge}.st = st(st >= goodEpoch.start(ge) & st < goodEpoch.end(ge));
GE{ge}.et = et(et > goodEpoch.start(ge) & et <= goodEpoch.end(ge));
eventDist{ge} = [GE{ge}.et - GE{ge}.st];
noEventDist{ge} = [GE{ge}.st; goodEpoch.end(ge)] - [goodEpoch.start(ge); GE{ge}.et];
% build shuffle cell (SC) array to shuffle noEvents (0) and events(1) separately
SC0{ch}{ge} = cell(1,length(noEventDist{ge}));
SC1{ch}{ge} = cell(1,length(eventDist{ge}));
for k = 1:length(SC0{ch}{ge}) % loop over noEvents
SC0{ch}{ge}{k} = logical(zeros(1,noEventDist{ge}(k)));
end
for k = 1:length(SC1{ch}{ge}) % loop over vents
SC1{ch}{ge}{k} = logical(ones(1,eventDist{ge}(k)));
end
end % of loop over good epochs
end % of loop over channels
% second set of loops for actual permutation test
numIter = 10000; % number of iterations for permutation test
randLogidx{i} = logical(zeros(size(logidx{i}))); % reset randLogidx
randContMat{i} = zeros(numIter,length(All_spindle_info{i}.eventInfo),length(All_spindle_info{i}.eventInfo)); % setup surrogate contingency matrix
for j = 1:numIter % surrogate permutation loop
for ch = 1:length(All_spindle_info{i}.eventInfo) % loop over channels
display([gcfg.subjectNames{i} ', channel ' All_spindle_info{i}.extractchannel{ch} ', surrogate iteration' num2str(j)]);
for ge = 1:length(goodEpoch.start) % loop over good epochs (GE, ge)
% shuffle indices for SC0 and SC1
randIdx_SC0{ch}{ge} = randperm(length(SC0{ch}{ge}));
randIdx_SC1{ch}{ge} = randperm(length(SC1{ch}{ge}));
% rebuild surrogate logindex
SCN{ch}{ge} = cell(1,length(SC0{ch}{ge})+length(SC1{ch}{ge}));
SCN{ch}{ge}(1:2:end) = SC0{ch}{ge}(randIdx_SC0{ch}{ge});
SCN{ch}{ge}(2:2:end) = SC1{ch}{ge}(randIdx_SC1{ch}{ge});
% make logical array and add missing sample point...(?)
zerofill = zeros(1,length(randLogidx{i}(ch,goodEpoch.start(ge):goodEpoch.end(ge)))-length([SCN{ch}{ge}{:}]));
randLogidx{i}(ch,goodEpoch.start(ge):goodEpoch.end(ge)) = [[SCN{ch}{ge}{:}] zerofill];
end % of loop over good epochs
end % of loop over channels
% build surrogate contingency table for
% randContMat{i}{j} = zeros(length(All_spindle_info{i}.eventInfo),length(All_spindle_info{i}.eventInfo)); % setup contingency matrix
for ch = 1:length(All_spindle_info{i}.eventInfo) % second loop over channels to test for condingencies (i.e. overlapping events)
tempContMat{i}{ch} = zeros(length(All_spindle_info{i}.eventInfo(ch).startTime),length(All_spindle_info{i}.eventInfo));
for e = 1:length(All_spindle_info{i}.eventInfo(ch).startTime) % loop over events
tempContMat{i}{ch}(e,:) = sum(randLogidx{i}(:,All_spindle_info{i}.eventInfo(ch).startTime(e):All_spindle_info{i}.eventInfo(ch).endTime(e)),2) > 0';
end % of loop over events
randContMat{i}(j,ch,:) = mean(tempContMat{i}{ch},1);
end % of second loop over channels
end % of surrogate permutation loop
% permutation test
sortRandContMat{i} = sort(randContMat{i},1);
for m = 1:size(sortRandContMat{i},2) % loop over rows
for n = 1:size(sortRandContMat{i},3) % loop over columns
pContMat{i}(n,m) = mean(squeeze(sortRandContMat{i}(:,m,n)) > contMat{i}(n,m)); % p-value
end
end
% save results
spindle_contingencies.contMat = contMat{i};
spindle_contingencies.pContMat = pContMat{i};
spindle_contingencies.randContMat = randContMat{i};
save('-v7.3', fullfile(gcfg.resultsPath,gcfg.subjectNames{i},[gcfg.subjectNames{i} '_spindle_' gcfg.spindle_timelockevent '_' gcfg.spindle_targetchannel{gcfg.subjects(i)} '_contingencies.mat']), 'spindle_contingencies');
% plot relevant contingency parameters
h3 = figure;
colormap hot;
subplot(2,2,1);
imagesc(squeeze(sortRandContMat{i}(1,:,:)));
title({[gcfg.subjectNames{i} ': MIN SURROGATE Spindle contingency matrix']});
set(gca,'clim',[0 1]);
colorbar;
set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'yDir','normal');
ylabel('Given a spindle in channel');
xlabel('there is a spindle in channel');
subplot(2,2,2);
imagesc(squeeze(sortRandContMat{i}(end,:,:)));
title({[gcfg.subjectNames{i} ': MAX SURROGATE Spindle contingency matrix']});
set(gca,'clim',[0 1]);
colorbar;
set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'yDir','normal');
ylabel('Given a spindle in channel');
xlabel('there is a spindle in channel');
subplot(2,2,3);
imagesc(pContMat{i});
title({[gcfg.subjectNames{i} ': P-values for Spindle contingency matrix']});
set(gca,'clim',[0 1]);
colorbar;
set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'yDir','normal');
ylabel('Given a spindle in channel');
xlabel('there is a spindle in channel');
subplot(2,2,4);
imagesc(contMat{i} .* (pContMat{i}<0.0001));
title({[gcfg.subjectNames{i} ': Significant (p < 0.0001) values in Spindle contingency matrix']});
set(gca,'clim',[0 1]);
colorbar;
set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'yDir','normal');
ylabel('Given a spindle in channel');
xlabel('there is a spindle in channel');
suptitle([gcfg.subjectNames{i} ': Contingency statistics with' num2str(numIter) ' iterations']);
set(h3, 'Name',[gcfg.subjectNames{i} '_spindle_' gcfg.spindle_timelockevent '_' gcfg.spindle_tsv_flag '_' gcfg.spindle_timelockchannel '_contingencySTATS_' gcfg.timestamp],'NumberTitle','off','units','normalized','outerposition',[0 0 1 1]);
filename = fullfile(gcfg.paths.results, gcfg.subjectNames{i}, [gcfg.subjectNames{i} '_spindle_' gcfg.spindle_timelockevent '_' gcfg.spindle_tsv_flag '_' gcfg.spindle_timelockchannel '_contingencySTATS_' gcfg.timestamp]);
saveas(h3,[filename '.fig']);
set(h3, 'PaperUnits', 'centimeters', 'PaperSize', [33.867 19.05], 'PaperPosition', [0 -1 33.867 19.05]); % [left bottom width height]
print(h3, '-dpdf', '-r300', [filename '.pdf']);
% % plot single-subject sorted surrogate figures
% figure;
% for sp = 1:min(12,numIter)
% subplot(3,4,sp)
% imagesc(squeeze(sortRandContMat{i}(sp,:,:)));
% colormap hot;
% set(gca,'clim',[0 1]);
% colorbar;
% set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
% set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',4);
% set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
% set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',4);
% set(gca,'yDir','normal');
% title({[gcfg.subjectNames{i} ': Spindle contingency matrix']});
% ylabel('Given a spindle in channel');
% xlabel('there is a spindle in channel');
% end
subjectToc{i} = toc;
display(['Contingency permutation test for subject ' gcfg.subjectNames{i} ' took ' num2str(subjectToc{i}) ' seconds.']);
end % of loop over subjects
elseif gcfg.loadPreviousContingencyResults == 1
for i = 1:numel(gcfg.subjects)
load(fullfile(gcfg.resultsPath,gcfg.subjectNames{i},[gcfg.subjectNames{i} '_spindle_' gcfg.spindle_timelockevent '_' gcfg.spindle_targetchannel{gcfg.subjects(i)} '_contingencies.mat']), 'spindle_contingencies');
contMat{i} = spindle_contingencies.contMat;
pContMat{i} = spindle_contingencies.pContMat;
randContMat{i} = spindle_contingencies.randContMat;
clear spindle_contingencies;
end
keyboard;
for i = 1:numel(gcfg.subjects)
numHCTargetChan(i) = find(strcmp(All_spindle_info{i}.timelockchannel, All_spindle_info{i}.extractchannel));
numCzTargetChan(i) = find(strcmp('Cz', All_spindle_info{i}.extractchannel));
for ch = 1:length(All_spindle_info{i}.eventInfo)
Cz2HCP(i) = contMat{i}(numCzTargetChan(i),numHCTargetChan(i));
Hc2CzP(i) = contMat{i}(numHCTargetChan(i),numCzTargetChan(i));
end
end
% paired t-test
[h,p,ci,stats] = ttest(Cz2HCP,Hc2CzP)
%% TEMP re-plotting for conference %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% plot relevant contingency parameters
h3r = figure;
colormap jet;
subplot(2,2,1);
imagesc(squeeze(sortRandContMat{i}(1,:,:)));
title({[gcfg.subjectNames{i} ': MIN SURROGATE Spindle contingency matrix']});
set(gca,'clim',[0 1]);
colorbar;
set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'yDir','normal');
ylabel('Given a spindle in channel');
xlabel('there is a spindle in channel');
subplot(2,2,2);
imagesc(squeeze(sortRandContMat{i}(end,:,:)));
title({[gcfg.subjectNames{i} ': MAX SURROGATE Spindle contingency matrix']});
set(gca,'clim',[0 1]);
colorbar;
set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'yDir','normal');
ylabel('Given a spindle in channel');
xlabel('there is a spindle in channel');
subplot(2,2,3);
imagesc(pContMat{i});
title({[gcfg.subjectNames{i} ': P-values for Spindle contingency matrix']});
set(gca,'clim',[0 1]);
colorbar;
set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'yDir','normal');
ylabel('Given a spindle in channel');
xlabel('there is a spindle in channel');
subplot(2,2,4);
imagesc(contMat{i} .* (pContMat{i}<0.0001));
title({[gcfg.subjectNames{i} ': Significant (p < 0.0001) values in Spindle contingency matrix']});
set(gca,'clim',[0 1]);
colorbar;
set(gca,'XTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'XTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'YTick',1:numel(All_spindle_info{i}.extractchannel));
set(gca,'YTickLabel',All_spindle_info{i}.extractchannel, 'FontSize',8);
set(gca,'yDir','normal');
ylabel('Given a spindle in channel');
xlabel('there is a spindle in channel');
suptitle([gcfg.subjectNames{i} ': Contingency statistics with' num2str(numIter) ' iterations']);
set(h3r, 'Name',[gcfg.subjectNames{i} '_spindle_' gcfg.spindle_timelockevent '_' gcfg.spindle_tsv_flag '_' gcfg.spindle_timelockchannel '_contingencySTATSjet_' gcfg.timestamp],'NumberTitle','off','units','normalized','outerposition',[0 0 1 1]);
filename = fullfile(gcfg.paths.results, gcfg.subjectNames{i}, [gcfg.subjectNames{i} '_spindle_' gcfg.spindle_timelockevent '_' gcfg.spindle_tsv_flag '_' gcfg.spindle_timelockchannel '_contingencySTATSjet_' gcfg.timestamp]);
saveas(h3r,[filename '.fig']);
set(h3r, 'PaperUnits', 'centimeters', 'PaperSize', [33.867 19.05], 'PaperPosition', [0 -1 33.867 19.05]); % [left bottom width height]
print(h3r, '-dpdf', '-r300', [filename '.pdf']);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end % of if statement deciding whether or not to load vs. calcualte contingencies
end % of function