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d181028_tuning_adhoc_permutation_and_multcomp.m
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d181028_tuning_adhoc_permutation_and_multcomp.m
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clear
% mice = [25,27,30,36,37,38,39,41,52,53,54,56,70,74,75,76];
% sessions = {[4,19],[3,16],[3,21],[1,17],[7],[2],[1,22],[3],[3,21],[3],[3],[3],[6],[4],[4],[4]};
mice = [38,41];
sessions = {[2],[3]};
baseDir = 'Y:\Whiskernas\JK\suite2p\';
%% for calcium
percentFailPerm = zeros(sum(cellfun(@(x) length(x), sessions)),1);
touchResponse = zeros(sum(cellfun(@(x) length(x), sessions)),1);
failNum = zeros(sum(cellfun(@(x) length(x), sessions)),1);
percentFailSharpness = zeros(sum(cellfun(@(x) length(x), sessions)),1);
for mi = 1 : length(mice)
% for mi = 6:length(mice)
cd([baseDir, sprintf('%03d',mice(mi))])
for si = 1 : length(sessions{mi})
mouse = mice(mi);
session = sessions{mi}(si);
fprintf('Processing JK%03d S%02d \n', mice(mi), sessions{mi}(si));
ufn = sprintf('UberJK%03dS%02d',mouse, session);
load(ufn)
% u = Uber.buildUberArray(mice(mi), sessions{mi}(si));
frameRate = u.frameRate;
fn = [u.mouseName,u.sessionName,'singleCell_anova_calcium.mat']; %
savefn = [u.mouseName,u.sessionName,'singleCell_anova_calcium_final.mat'];
permfn = [u.mouseName, u.sessionName, 'permtest_calcium.mat'];
load(fn);
load(permfn)
if length(fail) == length(cellsTuned) % meaning that permutation results are not applied yet
currentInd = sum(cellfun(@(x) length(x), sessions(1:(mi-1))))+1;
failNum(currentInd) = sum(fail);
percentFailPerm(currentInd) = sum(fail)/length(fail);
permfailInd = find(fail);
cellsFailPerm = cellsTuned(permfailInd);
changedToNTR = [];
changedToNTNR = [];
for ci = 1 : sum(fail)
cell = cellsTuned(permfailInd(ci));
cellind = find(cellsTotal == cell);
dF = cell2mat(dFtotal{cellind});
response = nanmean(dF(:,baseFrameNum+1:baseFrameNum+afterFrameNum),2);
if ttest(response)
tempThreshold = [max(thresholdResponsePositive, u.noise(cellid)), min(thresholdResponseNegative, -u.noise(cellid)/2)];
if mean(response) > tempThreshold(1) || mean(response) < tempThreshold(2)
changedToNTR = [changedToNTR; cell];
cellsNTResponse = [cellsNTResponse;cell];
tempTimeseries = nanmean(dF(:,baseFrameNum+1:baseFrameNum+afterFrameNum),1);
NTRAmplitude = [NTRAmplitude; abs(mean(response))];
if mean(response) > tempThreshold(1)
NTRdirection = [NTRdirection; 1]; % increase
mt = find(tempTimeseries > max(tempTimeseries)*0.9,1);
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; mt / frameRate];
elseif mean(response) < tempThreshold(2)
NTRdirection = [NTRdirection; 2]; % decrease
mt = find(tempTimeseries > min(tempTimeseries)*0.9,1);
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; mt / frameRate];
else
NTRdirection = [NTRdirection; 0]; % error
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; NaN];
end
% Response probability
responseNum = 0;
for ri = 1 : size(dF,1)
tempTS = dF(ri,baseFrameNum + 1 : baseFrameNum + afterFrameNum);
tempTS = tempTS(~isnan(tempTS));
[~, p] = ttest(tempTS');
if p < thresholdTtestResponse
if (mean(response) > tempThreshold(1) && mean(tempTS) > tempThreshold(1)) || ...
(mean(response) < tempThreshold(2) && mean(tempTS) < tempThreshold(2))
responseNum = responseNum + 1;
end
end
end
NTRresponseProb = [NTRresponseProb; responseNum/ri*100];
% Response reliability
template = nanmean(dF(:,baseFrameNum:end));
rho = zeros(size(dF,1),1);
for ri = 1 : size(dF,1)
tempTS = dF(ri,baseFrameNum:end);
inds = find(~isnan(tempTS));
rho(ri) = corr(template(inds)', tempTS(inds)');
end
NTRreliability = [NTRreliability; mean(rho)];
else
cellsNTNR = [cellsNTNR; cell];
changedToNTNR = [changedToNTNR; cell];
end
else
cellsNTNR = [cellsNTNR; cell];
changedToNTNR = [changedToNTNR; cell];
end
end
cellsTuned(permfailInd) = [];
tuneAmplitude(permfailInd) = [];
tuneAngle(permfailInd) = [];
tuneDirection(permfailInd) = [];
tuneMaxResponseTimepoint(permfailInd) = [];
tuneModulationMaxmin(permfailInd) = [];
tuneReliability(permfailInd) = [];
tuneResponseProb(permfailInd) = [];
tuneSharpness(permfailInd) = [];
tuneCateg = setdiff(tuneCateg, cellsFailPerm);
tuneLOO = setdiff(tuneLOO, cellsFailPerm);
tuneMM = setdiff(tuneMM, cellsFailPerm);
tuneRampStrict = setdiff(tuneRampStrict, cellsFailPerm);
touchResponse(currentInd) = length(changedToNTR);
cellsNTNR = sort(cellsNTNR);
[cellsNTResponse, sortind] = sort(cellsNTResponse);
NTRAmplitude = NTRAmplitude(sortind);
NTRdirection = NTRdirection(sortind);
NTRMaxResponseTimepoint = NTRMaxResponseTimepoint(sortind);
NTRresponseProb = NTRresponseProb(sortind);
NTRreliability = NTRreliability(sortind);
end
sharpfailInd = find(tuneSharpness == length(angles));
if ~isempty(sharpfailInd)
cellsFailSharp = cellsTuned(sharpfailInd);
percentFailPerm(currentInd) = length(sharpfailInd)/length(cellsTuned);
for ci = 1 : length(sharpfailInd)
cell = cellsTuned(sharpfailInd(ci));
cellind = find(cellsTotal == cell);
dF = cell2mat(dFtotal{cellind});
response = nanmean(dF(:,baseFrameNum+1:baseFrameNum+afterFrameNum),2);
if ttest(response)
tempThreshold = [max(thresholdResponsePositive, u.noise(cellid)), min(thresholdResponseNegative, -u.noise(cellid)/2)];
if mean(response) > tempThreshold(1) || mean(response) < tempThreshold(2)
changedToNTR = [changedToNTR; cell];
cellsNTResponse = [cellsNTResponse;cell];
tempTimeseries = nanmean(dF(:,baseFrameNum+1:baseFrameNum+afterFrameNum),1);
NTRAmplitude = [NTRAmplitude; abs(mean(response))];
if mean(response) > tempThreshold(1)
NTRdirection = [NTRdirection; 1]; % increase
mt = find(tempTimeseries > max(tempTimeseries)*0.9,1);
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; mt / frameRate];
elseif mean(response) < tempThreshold(2)
NTRdirection = [NTRdirection; 2]; % decrease
mt = find(tempTimeseries > min(tempTimeseries)*0.9,1);
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; mt / frameRate];
else
NTRdirection = [NTRdirection; 0]; % error
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; NaN];
end
% Response probability
responseNum = 0;
for ri = 1 : size(dF,1)
tempTS = dF(ri,baseFrameNum + 1 : baseFrameNum + afterFrameNum);
tempTS = tempTS(~isnan(tempTS));
[~, p] = ttest(tempTS');
if p < thresholdTtestResponse
if (mean(response) > tempThreshold(1) && mean(tempTS) > tempThreshold(1)) || ...
(mean(response) < tempThreshold(2) && mean(tempTS) < tempThreshold(2))
responseNum = responseNum + 1;
end
end
end
NTRresponseProb = [NTRresponseProb; responseNum/ri*100];
% Response reliability
template = nanmean(dF(:,baseFrameNum:end));
rho = zeros(size(dF,1),1);
for ri = 1 : size(dF,1)
tempTS = dF(ri,baseFrameNum:end);
inds = find(~isnan(tempTS));
rho(ri) = corr(template(inds)', tempTS(inds)');
end
NTRreliability = [NTRreliability; mean(rho)];
else
cellsNTNR = [cellsNTNR; cell];
changedToNTNR = [changedToNTNR; cell];
end
else
cellsNTNR = [cellsNTNR; cell];
changedToNTNR = [changedToNTNR; cell];
end
end
cellsTuned(sharpfailInd) = [];
tuneAmplitude(sharpfailInd) = [];
tuneAngle(sharpfailInd) = [];
tuneDirection(sharpfailInd) = [];
tuneMaxResponseTimepoint(sharpfailInd) = [];
tuneModulationMaxmin(sharpfailInd) = [];
tuneReliability(sharpfailInd) = [];
tuneResponseProb(sharpfailInd) = [];
tuneSharpness(sharpfailInd) = [];
tuneCateg = setdiff(tuneCateg, cellsFailSharp);
tuneLOO = setdiff(tuneLOO, cellsFailSharp);
tuneMM = setdiff(tuneMM, cellsFailSharp);
tuneRampStrict = setdiff(tuneRampStrict, cellsFailSharp);
touchResponse(currentInd) = length(changedToNTR);
cellsNTNR = sort(cellsNTNR);
[cellsNTResponse, sortind] = sort(cellsNTResponse);
NTRAmplitude = NTRAmplitude(sortind);
NTRdirection = NTRdirection(sortind);
NTRMaxResponseTimepoint = NTRMaxResponseTimepoint(sortind);
NTRresponseProb = NTRresponseProb(sortind);
NTRreliability = NTRreliability(sortind);
end
save(savefn, 'cell*','tune*','NTR*', 'dFtotal', '*ctype', 'angles', 'baseFrameNum', 'afterFrameNum', 'threshold*', ...
'excludeDrinkingTime', 'onlyBeforeDecision', 'onlyAfterDecision', 'allowOverlap', 'onlyFirstTouch', 'ksh*', 'ksp*', 'leveneTest', 'frameRate', 'oneSampleH', '*P', 'noise', 'c2*points', 'fov*',...
'changed*', '*fail*', 'anovaP', 'permmaxmod', 'touchResponse', 'percentFail*')
end
end
%% for spikes
percentFailPerm = zeros(sum(cellfun(@(x) length(x), sessions)),1);
touchResponse = zeros(sum(cellfun(@(x) length(x), sessions)),1);
failNum = zeros(sum(cellfun(@(x) length(x), sessions)),1);
percentFailSharpness = zeros(sum(cellfun(@(x) length(x), sessions)),1);
for mi = 1 : length(mice)
% for mi = 6:length(mice)
cd([baseDir, sprintf('%03d',mice(mi))])
for si = 1 : length(sessions{mi})
mouse = mice(mi);
session = sessions{mi}(si);
fprintf('Processing JK%03d S%02d \n', mice(mi), sessions{mi}(si));
ufn = sprintf('UberJK%03dS%02d',mouse, session);
load(ufn)
% u = Uber.buildUberArray(mice(mi), sessions{mi}(si));
frameRate = u.frameRate;
fn = [u.mouseName,u.sessionName,'singleCell_anova_spk.mat']; %
savefn = [u.mouseName,u.sessionName,'singleCell_anova_spk_final.mat'];
permfn = [u.mouseName, u.sessionName, 'permtest_spk.mat'];
load(fn);
load(permfn)
if length(fail) == length(cellsTuned) % meaning that permutation results are not applied yet
currentInd = sum(cellfun(@(x) length(x), sessions(1:(mi-1))))+1;
failNum(currentInd) = sum(fail);
percentFailPerm(currentInd) = sum(fail)/length(fail);
permfailInd = find(fail);
cellsFailPerm = cellsTuned(permfailInd);
changedToNTR = [];
changedToNTNR = [];
for ci = 1 : sum(fail)
cell = cellsTuned(permfailInd(ci));
cellind = find(cellsTotal == cell);
infspk = cell2mat(spkTotal{cellind});
response = nanmean(infspk(:,baseFrameNum+1:baseFrameNum+afterFrameNum),2);
if ttest(response)
tempThreshold = [max(thresholdResponsePositive, u.noise(cellid)), min(thresholdResponseNegative, -u.noise(cellid)/2)];
if mean(response) > tempThreshold(1) || mean(response) < tempThreshold(2)
changedToNTR = [changedToNTR; cell];
cellsNTResponse = [cellsNTResponse;cell];
tempTimeseries = nanmean(infspk(:,baseFrameNum+1:baseFrameNum+afterFrameNum),1);
NTRAmplitude = [NTRAmplitude; abs(mean(response))];
if mean(response) > tempThreshold(1)
NTRdirection = [NTRdirection; 1]; % increase
mt = find(tempTimeseries > max(tempTimeseries)*0.9,1);
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; mt / frameRate];
elseif mean(response) < tempThreshold(2)
NTRdirection = [NTRdirection; 2]; % decrease
mt = find(tempTimeseries > min(tempTimeseries)*0.9,1);
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; mt / frameRate];
else
NTRdirection = [NTRdirection; 0]; % error
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; NaN];
end
% Response probability
responseNum = 0;
for ri = 1 : size(infspk,1)
tempTS = infspk(ri,baseFrameNum + 1 : baseFrameNum + afterFrameNum);
tempTS = tempTS(~isnan(tempTS));
[~, p] = ttest(tempTS');
if p < thresholdTtestResponse
if (mean(response) > tempThreshold(1) && mean(tempTS) > tempThreshold(1)) || ...
(mean(response) < tempThreshold(2) && mean(tempTS) < tempThreshold(2))
responseNum = responseNum + 1;
end
end
end
NTRresponseProb = [NTRresponseProb; responseNum/ri*100];
% Response reliability
template = nanmean(infspk(:,baseFrameNum:end));
rho = zeros(size(infspk,1),1);
for ri = 1 : size(infspk,1)
tempTS = infspk(ri,baseFrameNum:end);
inds = find(~isnan(tempTS));
rho(ri) = corr(template(inds)', tempTS(inds)');
end
NTRreliability = [NTRreliability; mean(rho)];
else
cellsNTNR = [cellsNTNR; cell];
changedToNTNR = [changedToNTNR; cell];
end
else
cellsNTNR = [cellsNTNR; cell];
changedToNTNR = [changedToNTNR; cell];
end
end
cellsTuned(permfailInd) = [];
tuneAmplitude(permfailInd) = [];
tuneAngle(permfailInd) = [];
tuneDirection(permfailInd) = [];
tuneMaxResponseTimepoint(permfailInd) = [];
tuneModulationMaxmin(permfailInd) = [];
tuneReliability(permfailInd) = [];
tuneResponseProb(permfailInd) = [];
tuneSharpness(permfailInd) = [];
tuneCateg = setdiff(tuneCateg, cellsFailPerm);
tuneLOO = setdiff(tuneLOO, cellsFailPerm);
tuneMM = setdiff(tuneMM, cellsFailPerm);
tuneRampStrict = setdiff(tuneRampStrict, cellsFailPerm);
touchResponse(currentInd) = length(changedToNTR);
cellsNTNR = sort(cellsNTNR);
[cellsNTResponse, sortind] = sort(cellsNTResponse);
NTRAmplitude = NTRAmplitude(sortind);
NTRdirection = NTRdirection(sortind);
NTRMaxResponseTimepoint = NTRMaxResponseTimepoint(sortind);
NTRresponseProb = NTRresponseProb(sortind);
NTRreliability = NTRreliability(sortind);
end
sharpfailInd = find(tuneSharpness == length(angles));
if ~isempty(sharpfailInd)
cellsFailSharp = cellsTuned(sharpfailInd);
percentFailPerm(currentInd) = length(sharpfailInd)/length(cellsTuned);
for ci = 1 : length(sharpfailInd)
cell = cellsTuned(sharpfailInd(ci));
cellind = find(cellsTotal == cell);
infspk = cell2mat(spkTotal{cellind});
response = nanmean(infspk(:,baseFrameNum+1:baseFrameNum+afterFrameNum),2);
if ttest(response)
tempThreshold = [max(thresholdResponsePositive, u.noise(cellid)), min(thresholdResponseNegative, -u.noise(cellid)/2)];
if mean(response) > tempThreshold(1) || mean(response) < tempThreshold(2)
changedToNTR = [changedToNTR; cell];
cellsNTResponse = [cellsNTResponse;cell];
tempTimeseries = nanmean(infspk(:,baseFrameNum+1:baseFrameNum+afterFrameNum),1);
NTRAmplitude = [NTRAmplitude; abs(mean(response))];
if mean(response) > tempThreshold(1)
NTRdirection = [NTRdirection; 1]; % increase
mt = find(tempTimeseries > max(tempTimeseries)*0.9,1);
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; mt / frameRate];
elseif mean(response) < tempThreshold(2)
NTRdirection = [NTRdirection; 2]; % decrease
mt = find(tempTimeseries > min(tempTimeseries)*0.9,1);
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; mt / frameRate];
else
NTRdirection = [NTRdirection; 0]; % error
NTRMaxResponseTimepoint = [NTRMaxResponseTimepoint; NaN];
end
% Response probability
responseNum = 0;
for ri = 1 : size(infspk,1)
tempTS = infspk(ri,baseFrameNum + 1 : baseFrameNum + afterFrameNum);
tempTS = tempTS(~isnan(tempTS));
[~, p] = ttest(tempTS');
if p < thresholdTtestResponse
if (mean(response) > tempThreshold(1) && mean(tempTS) > tempThreshold(1)) || ...
(mean(response) < tempThreshold(2) && mean(tempTS) < tempThreshold(2))
responseNum = responseNum + 1;
end
end
end
NTRresponseProb = [NTRresponseProb; responseNum/ri*100];
% Response reliability
template = nanmean(infspk(:,baseFrameNum:end));
rho = zeros(size(infspk,1),1);
for ri = 1 : size(infspk,1)
tempTS = infspk(ri,baseFrameNum:end);
inds = find(~isnan(tempTS));
rho(ri) = corr(template(inds)', tempTS(inds)');
end
NTRreliability = [NTRreliability; mean(rho)];
else
cellsNTNR = [cellsNTNR; cell];
changedToNTNR = [changedToNTNR; cell];
end
else
cellsNTNR = [cellsNTNR; cell];
changedToNTNR = [changedToNTNR; cell];
end
end
cellsTuned(sharpfailInd) = [];
tuneAmplitude(sharpfailInd) = [];
tuneAngle(sharpfailInd) = [];
tuneDirection(sharpfailInd) = [];
tuneMaxResponseTimepoint(sharpfailInd) = [];
tuneModulationMaxmin(sharpfailInd) = [];
tuneReliability(sharpfailInd) = [];
tuneResponseProb(sharpfailInd) = [];
tuneSharpness(sharpfailInd) = [];
tuneCateg = setdiff(tuneCateg, cellsFailSharp);
tuneLOO = setdiff(tuneLOO, cellsFailSharp);
tuneMM = setdiff(tuneMM, cellsFailSharp);
tuneRampStrict = setdiff(tuneRampStrict, cellsFailSharp);
touchResponse(currentInd) = length(changedToNTR);
cellsNTNR = sort(cellsNTNR);
[cellsNTResponse, sortind] = sort(cellsNTResponse);
NTRAmplitude = NTRAmplitude(sortind);
NTRdirection = NTRdirection(sortind);
NTRMaxResponseTimepoint = NTRMaxResponseTimepoint(sortind);
NTRresponseProb = NTRresponseProb(sortind);
NTRreliability = NTRreliability(sortind);
end
save(savefn, 'cell*','tune*','NTR*', 'spkTotal', '*ctype', 'angles', 'baseFrameNum', 'afterFrameNum', 'threshold*', ...
'excludeDrinkingTime', 'onlyBeforeDecision', 'onlyAfterDecision', 'allowOverlap', 'onlyFirstTouch', 'ksh*', 'ksp*', 'leveneTest', 'frameRate', 'oneSampleH', '*P', 'noise', 'c2*points', 'fov*',...
'changed*', '*fail*', 'anovaP', 'permmaxmod', 'touchResponse', 'percentFail*')
end
end