dfa for XPprepostSWR XPtrigAvgRip pctILB rewTrigSWRXP ripPos template

DFAnalysis/dfa_XPprepostSWR.m

@@ -0,0 +1,127 @@
+
+
+function out = dfa_XPprepostSWR(idx, timeFilter, varargin)
+% get XP offset, pre and post SWR
+% use with singledayanal
+% DR_2020-09-30
+
+fprintf('day %d \n',idx(1))
+reqData = {'ca1rippleskons', 'lick'};
+check_required(reqData, varargin)
+
+run_shuffle = 1;
+eventType = 'ca1rippleskons';
+if ~isempty(varargin)
+    assign(varargin{:});
+end
+
+out = init_out(); % init output
+out.index = idx;
+out.animal = animal;
+day = idx(1);
+eps = idx(2:end);
+%% Get SWRs in timeFilter
+
+evid = find(contains(varargin(1:2:end), eventType));
+o = [1:2:length(varargin)]+1;
+swr = varargin{o(evid)};
+swrTimes = [];
+maxthresh = [];
+swrEnd = [];
+for e = 1:length(eps)
+    ep = eps(e);
+    try
+        swrTimes = [swrTimes; swr{day}{ep}{1}.starttime];
+        maxthresh = [maxthresh; swr{day}{ep}{1}.maxthresh];
+        swrEnd = [swrEnd; swr{day}{ep}{1}.endtime];
+    catch
+        try
+            swrTimes = [swrTimes; swr{day}{ep}.starttime];
+            maxthresh = [maxthresh; swr{day}{ep}.maxthresh];
+            swrEnd = [swrEnd; swr{day}{ep}.endtime];
+        catch
+            fprintf('no swr events detected for day%d ep%d\n', day, ep)
+            return
+        end
+    end
+end
+% apply timefilter to swrs
+incSWRs = ~isIncluded(swrTimes(:,1), timeFilter);
+fprintf('%d of %d swr events discarded bc excluded periods in timefilter: d%d\n',...
+    sum(incSWRs), length(incSWRs), day)
+swrTimes = swrTimes(incSWRs,:);
+% out.maxthresh = maxthresh;
+% out.swrEnd = swrEnd;
+
+if isempty(swrTimes)
+    return
+end
+
+%% Get licks in lick-burst intervals
+[intraBoutXP, boutTimes] = getLickBoutLicks(animal, [repmat(day,length(eps),1) eps'], ...
+    varargin{:});
+boutTimes = cell2mat({boutTimes{day}{eps}}');
+intraBoutXP = cell2mat({intraBoutXP{day}{eps}}');
+intraBoutXP = intraBoutXP(:,1);
+fprintf('%d XP within %d bursts \n', numel(intraBoutXP), size(boutTimes,1))
+
+
+%% get xp pre post swr
+% get swr events within lick-burst intervals
+burstSWRTimes = swrTimes(isIncluded(swrTimes, boutTimes));
+burstSWRTimes = sort(burstSWRTimes(~isnan(burstSWRTimes)));
+fprintf(' %d swrs within %d lickbouts. (%.02f pct swrs) \n', size(boutTimes,1), ...
+    numel(burstSWRTimes), length(burstSWRTimes)/length(swrTimes)*100)
+if isempty(burstSWRTimes)
+    fprintf('no swrs in lick bouts for %d %d.. skipping\n', day, ep)
+    return
+end
+% Get the swr-containing licks
+% histc given licks as edges: get bin idx. lickedges(binidx) is the prior edge of bin, 
+% aka the swr-preceding lick 
+% [~,~,swrLickBinidx] = histcounts(burstSWRTimes, intraBoutXP);
+% 
+% % time since last lick
+% swrTimeSinceLick = burstSWRTimes - intraBoutXP(swrLickBinidx);
+% if any(swrTimeSinceLick > .250)
+%     error('wut')
+% end
+% swr-containing ILI
+for b = 1:length(burstSWRTimes)
+    XPpreSWR(b,1) = max(intraBoutXP(intraBoutXP<burstSWRTimes(b)));
+    XPpostSWR(b,1) = min(intraBoutXP(intraBoutXP>=burstSWRTimes(b)));
+end
+XPpreSWR_offset = burstSWRTimes - XPpreSWR;
+XPpostSWR_offset = burstSWRTimes - XPpostSWR;
+
+if run_shuffle
+    r = rand(length(XPpreSWR),1);
+    ILI = XPpostSWR - XPpreSWR; % ILI
+    SWRtimes_shuf = XPpreSWR + (ILI .* r);% rand fraction of each ILI as shuf swr
+    XPpreSWR_offset_shuf = SWRtimes_shuf - XPpreSWR;
+    XPpostSWR_offset_shuf = SWRtimes_shuf - XPpostSWR;
+end
+
+out.XPpreSWR = XPpreSWR;
+out.XPpostSWR = XPpostSWR;
+out.XPpreSWR_offset = XPpreSWR_offset;
+out.XPpostSWR_offset = XPpostSWR_offset;
+out.XPpreSWR_offset_shuf = XPpreSWR_offset_shuf;
+out.XPpostSWR_offset_shuf = XPpostSWR_offset_shuf;
+out.SWRTimes_iLB = burstSWRTimes;
+out.XPTimes_iLB = intraBoutXP;
+end
+
+function out = init_out()
+out.index = [];
+out.animal = [];
+
+out.XPpreSWR = [];
+out.XPpostSWR = [];
+out.XPpreSWR_offset = [];
+out.XPpostSWR_offset = [];
+out.XPpreSWR_offset_shuf = [];
+out.XPpostSWR_offset_shuf = [];
+out.SWRTimes_iLB = [];
+out.XPTimes_iLB = [];
+end

DFAnalysis/dfa_XPtrigAvgRip.m

@@ -0,0 +1,93 @@
+
+function out = dfa_XPtrigAvgRip(idx, timeFilter, varargin)
+% get XP trig avg of rip power
+% use with singledayanal
+% DR_2020-09-30
+
+fprintf('day %d \n',idx(1))
+reqData = {'ca1rippleskons', 'lick'};
+check_required(reqData, varargin)
+
+win = [-.5 .5];
+eventType = 'ca1rippleskons';
+srate = 1500;
+if ~isempty(varargin)
+    assign(varargin{:});
+end
+
+out = init_out(); % init output
+out.index = idx;
+out.animal = animal;
+day = idx(1);
+eps = idx(2:end);
+
+%% get rip pwr trace
+evid = find(contains(varargin(1:2:end), eventType));
+o = [1:2:length(varargin)]+1;
+swr = varargin{o(evid)};
+
+rippwr = [];
+time = [];
+
+for e = 1:eps
+    rippwr = [rippwr; swr{day}{eps(e)}{1}.powertrace'];
+    time = [time; swr{day}{eps(e)}{1}.eegtimesvec_ref'];
+end
+
+% zscore
+rippwr = rippwr';
+zrippwr = ((rippwr - nanmean(rippwr))./nanstd(rippwr));
+
+%% Get licks in lick-burst intervals
+[intraBoutXP, boutTimes] = getLickBoutLicks(animal, [repmat(day,length(eps),1) eps'], ...
+    varargin{:});
+boutTimes = cell2mat({boutTimes{day}{eps}}');
+intraBoutXP = cell2mat({intraBoutXP{day}{eps}}');
+intraBoutXP = intraBoutXP(:,1);
+fprintf('%d XP within %d bursts \n', numel(intraBoutXP), size(boutTimes,1))
+
+% for each iLB XP, get a zrippwr trace within window
+% return this stack
+% also return the nanmean and nanstd of the stack
+zrippwr_XPtrig = [];
+rippwr_XPtrig = [];
+for iXP = 1:length(intraBoutXP)
+    xptimeIdx = min(find(time>=intraBoutXP(iXP)));
+    if diff([intraBoutXP(iXP) time(xptimeIdx)]) > .001
+        sprintf('%.03f diff, skipping',diff([intraBoutXP(iXP) time(xptimeIdx)]))
+        continue
+    end
+    startIdx = xptimeIdx-abs(win(1)*srate)-1;
+    endIdx = xptimeIdx+abs(win(2)*srate);
+    try
+        zrippwr_XPtrig = [zrippwr_XPtrig; zrippwr(startIdx:endIdx)];
+        rippwr_XPtrig = [rippwr_XPtrig; rippwr(startIdx:endIdx)];
+    catch
+        disp('window exceeds bounds, skipping')
+        continue
+    end
+end
+
+out.zrippwr_XPtrig = zrippwr_XPtrig;
+out.mean_zrippwr_XPtrig = nanmean(zrippwr_XPtrig,1);
+out.sem_zrippwr_XPtrig = nanstd(zrippwr_XPtrig,1)/sqrt(size(zrippwr_XPtrig,1));
+out.rippwr_XPtrig = rippwr_XPtrig;
+out.mean_rippwr_XPtrig = nanmean(rippwr_XPtrig,1);
+out.sem_rippwr_XPtrig = nanstd(rippwr_XPtrig,1)/sqrt(size(rippwr_XPtrig,1));
+out.win = win;
+out.srate = srate;
+out.time = linspace(win(1),win(2),length(out.mean_zrippwr_XPtrig));
+end
+
+function out = init_out()
+out.index = [];
+out.animal = [];
+out.time = [];
+
+out.zrippwr_XPtrig = [];
+out.mean_zrippwr_XPtrig = [];
+out.sem_zrippwr_XPtrig = [];
+out.rippwr_XPtrig = [];
+out.mean_rippwr_XPtrig = [];
+out.sem_rippwr_XPtrig = [];
+end

DFAnalysis/dfa_pctILB.m

@@ -0,0 +1,97 @@
+function out = dfa_pctILB(idx, timeFilter, varargin)
+% get pct swr iLB vs eLB
+% use with singledayanal
+% notebook: pctILB_2020_10_02.m
+% DR_2020-10-02
+
+fprintf('day %d \n',idx(1))
+reqData = {'ca1rippleskons', 'lick'};
+check_required(reqData, varargin)
+
+stdthresh = [2 4 6 8];
+eventType = 'ca1rippleskons';
+if ~isempty(varargin)
+    assign(varargin{:});
+end
+
+out = init_out(); % init output
+out.index = idx;
+out.animal = animal;
+day = idx(1);
+eps = idx(2:end);
+
+%% Get SWRs in timeFilter
+
+evid = find(contains(varargin(1:2:end), eventType));
+o = [1:2:length(varargin)]+1;
+swr = varargin{o(evid)};
+swrTimes = [];
+maxthresh = [];
+swrEnd = [];
+for e = 1:length(eps)
+    ep = eps(e);
+    try
+        swrTimes = [swrTimes; swr{day}{ep}{1}.starttime];
+        maxthresh = [maxthresh; swr{day}{ep}{1}.maxthresh];
+        swrEnd = [swrEnd; swr{day}{ep}{1}.endtime];
+    catch
+        try
+            swrTimes = [swrTimes; swr{day}{ep}.starttime];
+            maxthresh = [maxthresh; swr{day}{ep}.maxthresh];
+            swrEnd = [swrEnd; swr{day}{ep}.endtime];
+        catch
+            fprintf('no swr events detected for day%d ep%d\n', day, ep)
+            return
+        end
+    end
+end
+% apply timefilter to swrs
+incSWRs = ~isIncluded(swrTimes(:,1), timeFilter);
+fprintf('%d of %d swr events discarded bc excluded periods in timefilter: d%d\n',...
+    sum(incSWRs), length(incSWRs), day)
+swrTimes = swrTimes(incSWRs,:);
+
+maxthresh = maxthresh(incSWRs);
+if isempty(swrTimes)
+    return
+end
+
+%% Get licks in lick-burst intervals
+[intraBoutXP, boutTimes] = getLickBoutLicks(animal, [repmat(day,length(eps),1) eps'], ...
+    varargin{:});
+boutTimes = cell2mat({boutTimes{day}{eps}}');
+% fprintf('%d lick bursts \n', size(boutTimes,1))
+
+%% get iLB swrs
+
+for istd = 1:length(stdthresh)
+    stdidx = maxthresh > stdthresh(istd);
+    swrTimes_std = swrTimes(stdidx);
+    burstSWRTimes = swrTimes_std(isIncluded(swrTimes_std, boutTimes));
+%     burstSWRTimes = sort(burstSWRTimes(~isnan(burstSWRTimes)));
+    fprintf('::>%d Thresh:: %d of %d swrs within %d lickbouts. (%.02f pct swrs) \n', ...
+        stdthresh(istd), numel(burstSWRTimes), numel(swrTimes_std), size(boutTimes,1),...
+        length(burstSWRTimes)/length(swrTimes_std)*100)
+%     if isempty(burstSWRTimes)
+%         fprintf('no swrs in lick bouts for %d %d.. \n', day, ep)
+%         keyboard
+%     end
+
+    out.numSWR(istd) = length(swrTimes_std);
+    out.numSWRiLB(istd) = length(burstSWRTimes);
+    out.burstSWRTimes{istd} = burstSWRTimes;
+    out.pctSWRiLB(istd) = length(burstSWRTimes)/length(swrTimes_std)*100;
+%     out.maxthresh = maxthresh;
+end
+end
+
+
+function out = init_out()
+out.index = [];
+out.animal = [];
+out.numSWR = [];
+out.numSWRiLB = [];
+out.burstSWRTimes = [];
+out.pctSWRiLB = [];
+% out.maxthresh = [];
+end