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d181030_spatial_clustering_index_withdepth.m
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d181030_spatial_clustering_index_withdepth.m
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clear
mice = [25,27,30,36,37,39,52,53,54,56];
sessions = {[4,19],[3,16],[3,21],[1,17],[7],[1,22],[3,21],[3],[3],[3]};
baseDir = 'D:\TPM\JK\suite2p\';
positiveOnly = 1;
negativeOnly = 0;
c2only = 1;
% range = [1, 136, 243, 350, 700];
range = [1, 136, 350, 700]; % for L2, L3, L4
layerGroup = {[2],[3],[4],[2:3],[2,4],[3,4],[2:4]};
% % layers = 2:4; % layers = 2; layers = 3; layers = 2:3; layers = 4;
permLength = 10000;
for mi = 1 : length(mice)
mouse = mice(mi);
for si = 1 : length(sessions{mi})
session = sessions{mi}(si);
resultsfn = sprintf('JK%03dS%02dsingleCell_anova_FT_1secB_absthresh02_perm_sharp.mat', mouse, session);
savefn = sprintf('JK%03dS%02dsingleCell_spatial_clustering_index_withdepth_c2only.mat', mouse, session);
targetDir = sprintf('%s%03d',baseDir,mouse);
ufn = sprintf('UberJK%03dS%02d.mat',mouse,session);
cd(targetDir)
load(resultsfn, 'cell*', 'tune*', 'angles')
load(ufn)
clear cell
if positiveOnly
tuneIndsTotal = find(ismember(cellsTotal, cellsTuned(tuneDirection == 1)));
else
if negativeOnly
else
tuneIndsTotal = find(ismember(cellsTotal, cellsTuned));
end
end
sci = zeros(length(layerGroup),1);
sciperm = cell(length(layerGroup),1);
scipval = zeros(length(layerGroup),1);
for li = 1 : length(layerGroup)
layers = layerGroup{li};
if length(layers) < 3
currDepthInds = [];
for i = 1 : length(layers)
currDepthInds = [currDepthInds, find(cellDepths > range(layers(i)-1) & cellDepths <= range(layers(i)))];
end
tuneInds = intersect(tuneIndsTotal, currDepthInds);
end
if c2only
tuneInds = intersect(tuneInds, find(cellisC2));
end
cellsTunedInds = find(ismember(cellsTuned, cellsTotal(tuneInds)));
tuneAngles = tuneAngle(cellsTunedInds);
withinGroupDist = cell(length(angles),1);
betweenGroupDist = cell(length(angles)-1,1);
for i = 1 : length(angles)
currAngleInd = find(tuneAngles == angles(i));
if length(currAngleInd) > 1
currAngleComb = combnk(currAngleInd,2);
withinGroupDist{i} = zeros(size(currAngleComb,1),1);
for j = 1 : length(withinGroupDist{i})
ind1 = tuneInds(currAngleComb(j,1));
ind2 = tuneInds(currAngleComb(j,2));
withinGroupDist{i}(j) = sqrt((((celly(ind1) - celly(ind2))^2 + (cellx(ind1) - cellx(ind2))^2) * u.pixResolution)^2 + (cellDepths(ind1) - cellDepths(ind2))^2);
end
else
withinGroupDist{i} = [];
end
end
for i = 1 : length(angles)-1
currAngleInd = find(tuneAngles == angles(i));
if isempty(currAngleInd)
betweenGroupDist{i} = [];
else
currOtherInd = [];
for j = i+1 : length(angles)
currOtherInd = [currOtherInd; find(tuneAngles == angles(j))];
end
if isempty(currOtherInd)
betweenGroupDist{i} = [];
else
betweenGroupDist{i} = zeros(length(currAngleInd) * length(currOtherInd),1);
for j = 1 : length(currAngleInd)
ind1 = tuneInds(currAngleInd(j));
for k = 1 : length(currOtherInd)
ind2 = tuneInds(currOtherInd(k));
betweenGroupDist{i}((j-1)*length(currOtherInd) + k) = sqrt((((celly(ind1) - celly(ind2))^2 + (cellx(ind1) - cellx(ind2))^2) * u.pixResolution)^2 + (cellDepths(ind1) - cellDepths(ind2))^2);
end
end
end
end
end
withinGroupDistMean = mean(cell2mat(withinGroupDist));
betweenGroupDistMean = mean(cell2mat(betweenGroupDist));
sci(li) = betweenGroupDistMean / withinGroupDistMean;
tempsciperm = zeros(permLength,1);
parfor pi = 1 : permLength
permTuneAngles = tuneAngles(randperm(length(tuneAngles)));
pwithinGroupDist = cell(length(angles),1);
pbetweenGroupDist = cell(length(angles)-1,1);
for i = 1 : length(angles)
currAngleInd = find(permTuneAngles == angles(i));
if length(currAngleInd) > 1
currAngleComb = combnk(currAngleInd,2);
pwithinGroupDist{i} = zeros(size(currAngleComb,1),1);
for j = 1 : length(pwithinGroupDist{i})
ind1 = tuneInds(currAngleComb(j,1));
ind2 = tuneInds(currAngleComb(j,2));
pwithinGroupDist{i}(j) = sqrt((((celly(ind1) - celly(ind2))^2 + (cellx(ind1) - cellx(ind2))^2) * u.pixResolution)^2 + (cellDepths(ind1) - cellDepths(ind2))^2);
end
else
pwithinGroupDist{i} = [];
end
end
for i = 1 : length(angles)-1
currAngleInd = find(permTuneAngles == angles(i));
if isempty(currAngleInd)
pbetweenGroupDist{i} = [];
else
currOtherInd = [];
for j = i+1 : length(angles)
currOtherInd = [currOtherInd; find(permTuneAngles == angles(j))];
end
if isempty(currOtherInd)
pbetweenGroupDist{i} = [];
else
pbetweenGroupDist{i} = zeros(length(currAngleInd) * length(currOtherInd),1);
for j = 1 : length(currAngleInd)
ind1 = tuneInds(currAngleInd(j));
for k = 1 : length(currOtherInd)
ind2 = tuneInds(currOtherInd(k));
pbetweenGroupDist{i}((j-1)*length(currOtherInd) + k) = sqrt((((celly(ind1) - celly(ind2))^2 + (cellx(ind1) - cellx(ind2))^2) * u.pixResolution)^2 + (cellDepths(ind1) - cellDepths(ind2))^2);
end
end
end
end
end
pwithinGroupDistMean = mean(cell2mat(pwithinGroupDist));
pbetweenGroupDistMean = mean(cell2mat(pbetweenGroupDist));
tempsciperm(pi) = pbetweenGroupDistMean / pwithinGroupDistMean;
end
sciperm{li} = tempsciperm;
scipval(li) = length(find(sciperm{li} > sci(li))) / permLength;
end
save(savefn, 'sci*', 'range', 'layerGroup')
end
end