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Copy pathcoactPaper_figure06.m
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coactPaper_figure06.m
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function coactPaper_figure06()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=5;
letGapY=5;
fontsize=6;
close all
fh=initFig('width',18.6,'height',12.5,'font','Arial','fontsize',fontsize);
x=19;y=2;
panel_01(x,y,fontsize);
panelLetter2(x-letGapX-12,y-letGapY+4,alphabet(1,labelCase),'fontSize',labelSize,'isBold',labelWeight)
drawnow();
x=19+56;y=1;
panel_02(x,y,fontsize)
panelLetter2(x-letGapX-8,y-letGapY+2+3,alphabet(2,labelCase),'fontSize',labelSize,'isBold',labelWeight)
drawnow();
x=19+56+22.5*4+5;y=1+25;
panel_02sub(x,y,fontsize)
x=12;y=2+65;
panel_03(x,y,fontsize)
panelLetter2(x-letGapX-5,y-letGapY+1,alphabet(3,labelCase),'fontSize',labelSize,'isBold',labelWeight)
drawnow();
x=12;y=2+65+31;
panel_04(x,y,fontsize)
panelLetter2(x-letGapX-5,y-letGapY+1,alphabet(4,labelCase),'fontSize',labelSize,'isBold',labelWeight)
drawnow();
x=12+39;y=2+65+31;
panel_05(x,y,fontsize)
panelLetter2(x-letGapX-7,y-letGapY+1,alphabet(5,labelCase),'fontSize',labelSize,'isBold',labelWeight)
drawnow();
x=12+39+30;y=2+65;
panel_06(x,y,fontsize)
panelLetter2(x-letGapX-5,y-letGapY+1,alphabet(6,labelCase),'fontSize',labelSize,'isBold',labelWeight)
drawnow();
x=12+39+30+69;y=2+65;
panel_07(x,y,fontsize)
panelLetter2(x-letGapX-5,y-letGapY+1,alphabet(7,labelCase),'fontSize',labelSize,'isBold',labelWeight)
drawnow();
print(fh,sprintf('~/Dropbox/FearAnalyses/paper/figure/fig06_%s.pdf',datestr(now,'yyyymmdd')),'-dpdf','-painters','-r600')
end
function panel_01(x,y,fs)
for rIdx=1
if rIdx==1
basename='~/data/Fear/triple/maredsous200224/maredsous200224';
else
basename='~/data/Fear/triple/nostrum200304/nostrum200304';
end
load([basename '.basicMetaData.mat']);
pool(rIdx).basicMetaData=basicMetaData;
temp=load([basicMetaData.AnalysesName '-tripleCCG.mat']);
pool(rIdx).tripleCCG=temp.tripleCCG;
temp=load([basicMetaData.AnalysesName '-tripleAct.mat']);
pool(rIdx).tripleAct=temp.tripleAct;
temp=load([basicMetaData.Basename '.okUnit.spikes.mat']);
pool(rIdx).okUnit=temp.okUnit;
temp=load([basicMetaData.Basename '.ripples.events.mat']);
pool(rIdx).ripples=temp.ripples;
temp=load([basicMetaData.Basename '.amyHfo.events.mat']);
pool(rIdx).amyHFO=temp.amyHFO;
temp=load([basicMetaData.Basename '.pfcLowGamma.events.mat']);
pool(rIdx).pfcLowGamma=temp.pfcLowGamma;
temp=load([basicMetaData.Basename '.pfcGamma.events.mat']);
pool(rIdx).pfcGamma=temp.pfcGamma;
temp=matfile([basicMetaData.AnalysesName '-icaReac.mat']);
pool(rIdx).icaReac=temp.icaReac(1,2);
pool(rIdx).lfp=memmapfile(basicMetaData.lfp,'format',{'int16',[basicMetaData.nCh,basicMetaData.nSample.lfp],'x'});
pool(rIdx).chList=[basicMetaData.Ch.hpcTheta(1),basicMetaData.Ch.amyGamma(1),basicMetaData.Ch.pfcDelta(1)];
end
varList=fieldnames(pool);
swrFil = designfilt('bandpassfir','FilterOrder',1024, ...
'CutoffFrequency1',100,'CutoffFrequency2',250, ...
'SampleRate',1250);
hfoFil = designfilt('bandpassfir','FilterOrder',1024, ...
'CutoffFrequency1',90,'CutoffFrequency2',180, ...
'SampleRate',1250);
smCore=normpdf(-4:4,0,0.51);
smCore=smCore/sum(smCore);
[x1,x2] = meshgrid(-4:4,-4:4);
sm2dCore=mvnpdf([x1(:),x2(:)],[0,0],0.5*eye(2));
sm2dCore=reshape(sm2dCore/sum(sm2dCore),9,9);
cRange=[0,0.03];
yGap=1;
width=38;
xGap=10;
lfpHeight=20;
filtLfpHeight=10;
reactHeight=7;
rasterHeigth=15;
tWin=0.3;
showNM=false;
for rIdx=1
for vIdx=1:length(varList)
eval(sprintf('%s=pool(%d).%s;',varList{vIdx},rIdx,varList{vIdx}));
end
if rIdx==1
reacId=[3,9,20];evtID=47;
end
for n=1:3
singleIdx(n)=find(tripleCCG.regIdx{n}==reacId(n));
end
ccg3=squeeze(tripleCCG.ccg(singleIdx(1),singleIdx(2),singleIdx(3),:,:))/tripleCCG.nBin;
smCCG3=[fliplr(ccg3),ccg3,fliplr(ccg3)];
smCCG3=[flipud(smCCG3);smCCG3;fliplr(smCCG3)];
smCCG3=conv2(smCCG3,sm2dCore,'same');
smCCG3=smCCG3(size(ccg3,1)+(1:size(ccg3,1)),size(ccg3,2)+(1:size(ccg3,2)));
triIdx=find(all(abs(tripleAct.reactIdx-reacId)==0,2));
tShift=tripleAct.tShift(triIdx,:)*20;
t=tripleAct.timestamps{triIdx};
regList=tripleCCG.param.regList;
icaStr=zscore(icaReac.strength(reacId,:),[],2);
tbin=((1:size(icaStr,2))-0.5)*0.02;
tCenter=round(mean(t(evtID,:))/0.02)*0.02;
regName=pool(rIdx).basicMetaData.Ch.names((pool(rIdx).chList));
colTemp=setCoactColor();
col=zeros(length(regName),3);
for m=1:3
col(m,:)=colTemp.region.(strrep(regName{m},' ',''));
end
subplotInMM(x,y,width,lfpHeight)
hold on
lfpWinWidth=ceil(basicMetaData.SampleRates.lfp *tWin);
fRange=round(tCenter*basicMetaData.SampleRates.lfp)+(lfpWinWidth+2048)*[-1,1];
wav=0.194*double(lfp.Data.x(chList,fRange(1):fRange(2)));
for m=1:3
plot((-lfpWinWidth:lfpWinWidth)/basicMetaData.SampleRates.lfp*1e3,wav(m,2048+(1:lfpWinWidth*2+1))-750*(m-1),'color',col(m,:))
end
axis tight
xlim(tWin*1e3*[-1,1])
plot(-200+[0,0],-2100+[0,500],'k-')
text(-190,-2100+250,'0.5 mV','VerticalAlignment','middle')
for m=1:3
reg=strrep(regList{m},' ','');
regName=regList{m};
if strcmp(regName,'PrL L5')
regName='PL5';
end
text(-tWin*1e3*1.02,-750*(m-1),sprintf('\\color[rgb]{%f %f %f}%s wideband',...
colTemp.region.(reg),regName),'HorizontalAlignment','right','VerticalAlignment','middle')
end
axis off
subplotInMM(x,y+(lfpHeight)+yGap*1,width,filtLfpHeight)
hold on
fWav=zeros(size(wav));
for m=1:3
if m==1
fWav(m,:)=filtfilt(swrFil,wav(m,:));
else
fWav(m,:)=filtfilt(hfoFil,wav(m,:));
end
end
for m=1:3
plot((-lfpWinWidth:lfpWinWidth)/basicMetaData.SampleRates.lfp*1e3,fWav(m,2048+(1:lfpWinWidth*2+1))-200*(m-1),'color',col(m,:))
end
subEvt{1}=(ripples.timestamps(ripples.timestamps(:,2)>tCenter-tWin & ripples.timestamps(:,1)<tCenter+tWin,:)-tCenter)*1e3;
subEvt{2}=(amyHFO.timestamps(amyHFO.timestamps(:,2)>tCenter-tWin & amyHFO.timestamps(:,1)<tCenter+tWin,:)-tCenter)*1e3;
subEvt{3}=(pfcGamma(4).timestamps(pfcGamma(4).timestamps(:,2)>tCenter-tWin & pfcGamma(4).timestamps(:,1)<tCenter+tWin,:)-tCenter)*1e3;
axis tight
xlim(tWin*1e3*[-1,1])
plot(-200+[0,0],-350+[0,100],'k-')
text(-190,-325,'0.1 mV','VerticalAlignment','middle')
filName.vCA1='SWR';
filName.BLA='HFO';
filName.PrLL5='cRipple';
for m=1:3
reg=strrep(regList{m},' ','');
regName=regList{m};
if strcmp(regName,'PrL L5')
regName='PL5';
end
text(-tWin*1e3*1.02,-200*(m-1),sprintf('\\color[rgb]{%f %f %f}%s %s',...
colTemp.region.(reg),regName,filName.(reg)),'HorizontalAlignment','right','VerticalAlignment','middle')
end
axis off
subplotInMM(x,y+(lfpHeight+filtLfpHeight)+yGap*2,width,reactHeight)
hold on
cFrame=ceil((tCenter)/0.02);
for m=1:3
plot((-20:20)*20,icaStr(m,cFrame+[-20:20])-(m-1)*3,'-','color',col(m,:))
end
hold on
ax=fixAxis;
xlim(tWin*1e3*[-1,1])
ylabel('Reactivation strength','fontsize',fs,'FontWeight','normal')
ylim([-10,15])
plot(-200+[0,0],4+[0,10],'k-')
text(-190,9,'10 z','VerticalAlignment','middle')
axis off
subplotInMM(x,y+(lfpHeight+filtLfpHeight+reactHeight)+yGap*3,width,rasterHeigth)
tRange=tbin(cFrame)+tWin*[-1,1];
subSpk=okUnit.spikeTime(okUnit.spikeTime>tRange(1)&okUnit.spikeTime<tRange(2))-tbin(cFrame);
subClu=okUnit.cluster(okUnit.spikeTime>tRange(1)&okUnit.spikeTime<tRange(2));
spk=[];
clu=[];
nCell=0;
spkCol=[];
firedAllReg=unique(subClu);
colList=setCoactColor
for m=1:3
reg=icaReac.region{reacId(m)};
cID=find(strcmp(okUnit.cluInfo.region,reg));
fired=ismember(cID,firedAllReg);
wRank=icaReac.weigth{reacId(m)};
wRank=length(wRank)-tiedrank(wRank);
memb=wRank<5;
memb=memb(fired);
cID=cID(fired);
toUseM=ismember(okUnit.cluster,cID(memb))&okUnit.spikeTime>tRange(1)&okUnit.spikeTime<tRange(2);
toUseN=ismember(okUnit.cluster,cID(~memb))&okUnit.spikeTime>tRange(1)&okUnit.spikeTime<tRange(2);
for s=1:2
if s==1
toUse=toUseM;
colTemp=colList.region.(strrep(strrep(reg,' ',''),'/',''));
else
if ~showNM
continue
end
toUse=toUseN;
colTemp=colList.region.(strrep(strrep(reg,' ',''),'/',''));
colTemp=rgb2hsv(colTemp);
colTemp(2)=colTemp(2)/3;
colTemp(3)=1;
colTemp=hsv2rgb(colTemp);
end
[~,~,temp]=unique(okUnit.cluster(toUse));
if isempty(temp)
continue
end
tempN=max(temp);
colSpk((1:tempN)+nCell,:)=repmat(colTemp,tempN,1);
clu=[clu;temp+nCell];
nCell=nCell+tempN;
spk=[spk;okUnit.spikeTime(toUse)-tRange(1)];
end
end
scatter(spk,nCell-clu+0.5,36,colSpk(clu,:),'.')
hold on
xlim([0,diff(tRange)])
ylim([0,nCell])
plot(0.1+[0,50]/1e3,nCell/6+[0,0],'k-')
text(0.1+50/1e3/2,nCell/6,'50 ms','VerticalAlignment','top','HorizontalAlignment','center')
axis off
end
end
function panel_02(x,y,fs)
width=15;
height=width;
histHeight=12;
xRange=210*[-1,1];
yRange=210*[-1,1];
r2Range=[-0.01,0.07];
r3Range=[-0.005,0.025];
xGap=7.5;
yGap=7.5;
xGapAdd=18;
doubleSig=poolVar('icaReacCCG_sig.mat');
double=poolVar('icaReacZNCCG.mat');
triple=poolVar('tripleCCG.mat');
tripleSh=poolVar('tripleCCGsh.mat');
ratList=fieldnames(triple);
ratIdx=[13;8;12;14];
reactID=[3,9,20;
5,14,32;
1,3,7;
1,11,23];
smCore=normpdf(-4:4,0,1);
smCore=smCore/sum(smCore);
[x1,x2] = meshgrid(-2:2,-2:2);
sm2dCore=mvnpdf([x1(:),x2(:)],[0,0],0.5*eye(2));
sm2dCore=reshape(sm2dCore/sum(sm2dCore),5,5);
nDobBin=double.(ratList{1})(2).param.tWindow/double.(ratList{1})(2).param.tBinSize;
tDob=(-nDobBin:nDobBin)*double.(ratList{1})(2).param.tBinSize*1000;
dobTidx=find(abs(tDob)<=220);
tDob=tDob(dobTidx);
col=setCoactColor();
pos=[0,0
1,0
2,0
3,0
];
for idx=1:length(ratIdx)
rat=ratList{ratIdx(idx)};
for n=1:3
singleIdx(n)=find(triple.(rat).regIdx{n}==reactID(idx,n));
end
xPos=x+(width+xGap)*pos(idx,1);
yPos=y+(height+yGap)*pos(idx,2)+3;
subplotInMM(xPos,yPos,width,width)
hold on
triCCG=squeeze(triple.(rat).ccg(singleIdx(1),singleIdx(2),singleIdx(3),:,:))/triple.(rat).nBin;
ccgSize=size(triCCG);
shPeakVal=squeeze(tripleSh.(rat).peakVal(singleIdx(1),singleIdx(2),singleIdx(3),:))/triple.(rat).nBin;
peakVal=triple.(rat).peakVal(singleIdx(1),singleIdx(2),singleIdx(3))/triple.(rat).nBin;
tTri=(-(ccgSize(1)-1)/2:(ccgSize(2)-1)/2)*20;
triCCG=[fliplr(triCCG),triCCG,fliplr(triCCG)];
triCCG=[flipud(triCCG);triCCG;flipud(triCCG)];
triCCG=conv2(triCCG,sm2dCore,'same');
triCCG=triCCG(ccgSize(1)+(1:ccgSize(1)),ccgSize(2)+(1:ccgSize(2)));
imagescXY(tTri,tTri,triCCG)
plot(110*[1,1,0,-1,-1,0,1],110*[0,1,1,0,-1,-1,0],'w-')
plot(110*[1,1,0,-1,-1,0,1],110*[0,1,1,0,-1,-1,0],'w-')
plot(xRange,yRange,'w-')
plot(xRange,[0,0],'w-')
plot([0,0],yRange,'w-')
xlim(xRange)
ylim(yRange)
clim(r3Range)
if pos(idx,1)==0
ylabel('BLA - PL5 (ms)','fontsize',fs,'FontWeight','normal')
end
xlabel('vCA1 - PL5 (ms)','fontsize',fs,'FontWeight','normal')
subplotInMM(xPos,yPos+(height+yGap)*2-height/2,width,histHeight)
for idx1=1:3
idx2=mod(idx1,3)+1;
dIdx(idx1)=find(all(double.(rat)(2).pairID==reactID(idx,[idx1,idx2]),2)|all(double.(rat)(2).pairID==reactID(idx,[idx2,idx1]),2));
end
hold on
for n=1:3
dCCG=conv(double.(rat)(2).nrem.real.ccg(dIdx(n),:,3),smCore,'same');
pairCode=join(double.(rat)(2).region(double.(rat)(2).pairID(dIdx(n),:)),'');
pairCode=strrep(pairCode{1},' ','');
plot(tDob,dCCG(dobTidx),'color',col.pair.(pairCode))
end
ylim(r2Range)
xlim(xRange)
xlabel('\Delta time (ms)','fontsize',fs,'FontWeight','normal')
if pos(idx,1)==0
ylabel('CCG of partial-pair (r)','fontsize',fs,'FontWeight','normal')
end
ax=fixAxis;
pOrder=[1,3,2];
if pos(idx,1)==3
for n=1:3
pairName=join(double.(rat)(2).region(double.(rat)(2).pairID(dIdx(pOrder(n)),:)),' - ');
pairCode=join(double.(rat)(2).region(double.(rat)(2).pairID(dIdx(pOrder(n)),:)),'');
pairCode=strrep(pairCode{1},' ','')
text2(1.05,0.6+0.14*n,sprintf('\\color[rgb]{%f %f %f}%s',col.pair.(pairCode),strrep(pairName{1},'PrL ','P')))
end
end
if pos(idx,1)==3
subplotInMM(xPos+width+1,yPos,1.5,height)
imagesc([],r3Range,linspace(r3Range(1),r3Range(2),256)')
set(gca,'YDir','normal')
ylabel('Triple CCG (a.u.)','fontsize',fs,'FontWeight','normal')
yticks([r3Range(1),0.01,r3Range(2)])
yticklabels({['< ' num2str(r3Range(1))],0.01,['> ' num2str(r3Range(2))]})
set(gca,'YAxisLocation','right')
set(get(gca,'YLabel'),'Rotation',-90,'Position',get(get(gca,'ylabel'),'Position').*[1.2,1,1])
box off
end
subplotInMM(xPos,yPos,width,height)
fh=gcf;
ps=fh.PaperSize;
subplotInMM(xPos,yPos+(height+yGap)*1,width,height/2)
bin=0:0.005:ceil(max([peakVal;shPeakVal])/0.1)*0.1;
cnt=hist(shPeakVal,bin)/length(shPeakVal)*100;
patch([bin(end),bin(1),bin],[0,0,cnt],0.5*[1,1,1],'linestyle','none')
hold on
axis tight
yMax=ceil(max(cnt)/10)*10;
ylim([0,60])
yticks(0:20:60)
xlabel('Peak (a.u.)','FontSize',fs,'FontWeight','normal')
box off
xlim([0,0.25])
if pos(idx,1)==0
ylabel('%')
end
ax=fixAxis
plot(peakVal+[0,0],ax(3:4),'r-')
if pos(idx,1)==3
text2(1.05,0.3+0.28*2,'Actual',ax,'color','r')
text2(1.05,0.3+0.28,'Surrogates',ax,'color',0.5*[1,1,1])
end
end
end
function panel_02sub(x,y,fs)
insetWidth=13;
col=setCoactColor();
regName{1}=sprintf('\\color[rgb]{%f %f %f}C',col.region.vCA1);
regName{2}=sprintf('\\color[rgb]{%f %f %f}B',col.region.BLA);
regName{3}=sprintf('\\color[rgb]{%f %f %f}P',col.region.PrLL5);
subplotInMM(x,y,insetWidth,insetWidth)
hold on
plot(110*[-1,1],[0,0],'k-')
plot([0,0],110*[-1,1],'k-')
plot(110*[-1,1],110*[-1,1],'k-')
patch([0,1,1]*110,[-1,-1,0]*110,[0,0,0])
patch([-1,-1,0]*110,[0,1,1]*110,[0,0,0])
xlim(110*[-1,1])
ylim(110*[-1,1])
xticks([])
yticks([])
box on
legInfo=[-0.55,-0.275,1,2,3
-0.33, 0.35,1,3,2
0.4, 0.7,3,1,2
0.66, 0.33,3,2,1
0.4, -0.33,2,3,1
-0.275,-0.55,2,1,3];
for idx=1:6
text(legInfo(idx,1)*110,legInfo(idx,2)*110,join(regName(legInfo(idx,3:5)),''),...
'HorizontalAlignment','center','VerticalAlignment','middle','fontsize',fs,'Rotation',45)
end
regName{1}=sprintf('\\color[rgb]{%f %f %f}B:BLA',col.region.BLA);
regName{2}=sprintf('\\color[rgb]{%f %f %f}C:vCA1',col.region.vCA1);
regName{3}=sprintf('\\color[rgb]{%f %f %f}P:PL5',col.region.PrLL5);
ax=fixAxis;
for n=1:3
text2(0.4,-0.05-0.15*(n-1),regName{n},ax,'verticalAlign','top')
end
text2(0.5,1.35,'Activation',ax,'verticalAlign','top','horizontalAlign','center')
text2(0.5,1.20,'order',ax,'verticalAlign','top','horizontalAlign','center')
end
function panel_03(x,y,fs)
width=16;
height=16;
barWidth=18;
triple=poolVar('tripleCCG.mat');
ratList=fieldnames(triple);
sigT=[];
allT=[];
for ratIdx=1:length(ratList)
rat=ratList{ratIdx};
if isempty(triple.(rat).ccg)
continue
end
sigT=[sigT;triple.(rat).sig.tShift];
end
sigHist=histcounts2(sigT(:,1),sigT(:,2),-5.5:5.5,-5.5:5.5);
[xGrid,yGrid]=meshgrid(-5:5,-5:5);
fID=fopen('~/data/Fear/triple/analyses/paper/SourceData/fig06_c.csv','w');
fprintf(fID,'Fig. 6c\n\n');
fprintf(fID,'BLA - PL5 (ms),%s\n',joinNumVec(sigT(:,1)*20));
fprintf(fID,'vCA1 - PL5 (ms),%s\n',joinNumVec(sigT(:,2)*20));
fclose(fID);
[xPos,yPos]=find(abs(xGrid-yGrid)<=5);
xyPos=find(abs(xGrid-yGrid)<=5);
nPos=size(xPos,1);
halfStep=300;
nsHalfStep=floor(-log10(0.05)*100);
grad=[linspace(0,1,halfStep-nsHalfStep),ones(1,nsHalfStep),]
const=ones(1,halfStep);
sigCol=[grad,const
grad,fliplr(grad)
const,fliplr(grad)
]';
val=sigHist;
subplotInMM(x,y,width,height)
imagescXY(100*[-1,1],100*[-1,1],val/sum(val(:))*100)
expect=sum(val(:))/nPos;
chi2=sum((val(xyPos)-expect).^2/expect);
p=chi2cdf(chi2,nPos-1,'upper');
fprintf('p = %0.3e as uniform (chi square test)',p)
clim([0,7])
colormap(gca,hot)
xlabel('vCA1 - PL5 (ms)','fontsize',fs,'FontWeight','normal')
ylabel('BLA - PL5 (ms)','fontsize',fs,'FontWeight','normal')
box off
title('Triple CCG peak position','fontsize',fs,'fontweight','normal')
p=min((1-poisscdf(val,sum(val(:))/nPos))*nPos,1);
[sigX,sigY]=find(p<0.01);
if ~isempty(sigX)
sigY=(sigY-(size(p,1)+1)/2)*20;
sigX=(sigX-(size(p,2)+1)/2)*20;
for idx=1:length(sigX)
text(sigX(idx),sigY(idx)-7.5,'**','VerticalAlignment','middle','HorizontalAlignment','center')
end
end
ax=fixAxis;
hold on
plot(ax(1:2),[0,0],'c-')
plot([0,0],ax(3:4),'c-')
plot(ax(1:2),ax(3:4),'c-')
plot([ax(1),0],[0,ax(4)],'c-')
plot([0,ax(2)],[ax(3),0],'c-')
subplotInMM(x+width+1,y,1.5,height)
imagescXY([],[0,7],linspace(0,7,256))
colormap(gca,hot)
set(gca,'YAxisLocation','right')
xticks([])
textInMM(x+width+7,y+height/2,'Fraction of triplets (%)','horizontalAlign','center','Rotation',-90,'fontsize',fs)
box off
subplotInMM(x+width+17,y,barWidth,height);
col=setCoactColor();
regName{1}=sprintf('\\color[rgb]{%f %f %f}C',col.region.vCA1);
regName{2}=sprintf('\\color[rgb]{%f %f %f}B',col.region.BLA);
regName{3}=sprintf('\\color[rgb]{%f %f %f}P',col.region.PrLL5);
pList=sortrows(perms(1:3),'ascend');
sesIdx=1;
for pIdx=1:size(pList,1)
for n=1:3
idx(n)=find(pList(pIdx,:)==n);
end
if idx(1)<idx(3)
c1=sigT(:,1,sesIdx)<0;
else
c1=sigT(:,1,sesIdx)>0;
end
if idx(2)<idx(3)
c2=sigT(:,2,sesIdx)<0;
else
c2=sigT(:,2,sesIdx)>0;
end
if idx(1)<idx(2)
c3=sigT(:,1,sesIdx)<sigT(:,2,sesIdx);
else
c3=sigT(:,1,sesIdx)>sigT(:,2,sesIdx);
end
evtCnt(pIdx,sesIdx)=sum(c1&c2&c2&c3)
end
for n=1:6
cmbName{n}=[];
for m=1:3
cmbName{n}=[cmbName{n} regName{pList(n,m)}]
end
end
bar(1:6,evtCnt(:,sesIdx)/size(sigT,1)*100,0.5,'facecolor','k')
hold on
plot([0.25,6.75],(10/91)*100+[0,0],'-','color',0.5*[1,1,1])
fill([0.25,6.75,6.75,0.25],poissinv([0.025,0.025,0.975,0.975],100*10/91),...
0.5*[1,1,1],'linestyle','none','FaceAlpha',0.5)
p=poisscdf(evtCnt(:,sesIdx),100/91*10);
p(7)=poisscdf(size(sigT,1)-sum(evtCnt(:,sesIdx)),100/91*31);
p=1-abs(p-0.5)*2;
for n=1:7
if p(n)<0.001
sigTxt='***';
elseif p(n)<0.01
sigTxt='**';
elseif p(n)<0.05
sigTxt='*';
else
sigTxt='';
end
if ~isempty(sigTxt)
if n<7
yPos=evtCnt(n,sesIdx);
else
yPos=size(sigT,1)-sum(evtCnt(:,sesIdx));
end
text(n,yPos+1,sigTxt,...
'HorizontalAlignment','center','VerticalAlignment','middle','FontSize',fs)
end
end
set(gca,'XTick',1:6,'XTickLabel',cmbName,'XTickLabelRotation',-90)
xlim([0.25,6.75])
ylim([0,25])
ylabel('Fraction of triplets (%)','fontsize',fs,'FontWeight','normal')
xlabel('Activation order','fontsize',fs,'FontWeight','normal','fontsize',fs,'FontWeight','normal')
box off
end
function panel_04(x,y,fs)
width=20.5;
height=16;
double=poolVar('icaReacCCG_sig.mat');
triple=poolVar('tripleCCG.mat');
ratList=fieldnames(triple);
inDouble={};
inTriple={[],[],[]};
sigFrac=[];
for ratIdx=1:length(ratList)
rat=ratList{ratIdx};
if isempty(triple.(rat).sig.coact)
continue
end
dobIdx=double.(rat)(2).pairID(double.(rat)(2).nrem.significance(:,3)==1,:);
reg=double.(rat)(2).region(dobIdx);
dobIdx=dobIdx(~strcmp(reg(:,1),reg(:,2)),:);
reg=reg(~strcmp(reg(:,1),reg(:,2)),:);
triIdx=triple.(rat).sig.coact;
for idx=1:size(dobIdx,1)
if any(strcmp(reg(idx,:),'vCA1')) & any(strcmp(reg(idx,:),'PrL L5'))
typeIdx=1;
elseif any(strcmp(reg(idx,:),'BLA')) & any(strcmp(reg(idx,:),'PrL L5'))
typeIdx=2;
elseif any(strcmp(reg(idx,:),'vCA1')) & any(strcmp(reg(idx,:),'BLA'))
typeIdx=3;
else
continue
end
inTriple{typeIdx}(end+1)=any(sum(triIdx==dobIdx(idx,1) | triIdx==dobIdx(idx,2),2)==2);
end
inDob=[];
for idx=1:size(triIdx,1)
for type=1:3
switch type
case 1
n1=1;n2=2;
case 2
n1=2;n2=3;
case 3
n1=3;n2=1;
end
inDob(idx,type)=any((dobIdx(:,1)==triIdx(idx,n1)&dobIdx(:,2)==triIdx(idx,n2)) | ...
(dobIdx(:,2)==triIdx(idx,n1)&dobIdx(:,1)==triIdx(idx,n2)));
end
end
sigFrac(end+1,:)=[size(triple.(rat).sig.p,1),prod(size(triple.(rat).p))];
inDouble{end+1}=inDob;
end
colTemp=setCoactColor();
col=[colTemp.pair.vCA1PrLL5;colTemp.pair.BLAPrLL5;colTemp.pair.vCA1BLA];
pairList={'vCA1','PL5'
'BLA','PL5'
'vCA1','BLA'};
inTriFrac=cellfun(@mean,inTriple)*100
dobFrac=mean(cat(1,inDouble{:}))*100;
subplotInMM(x,y,width,height)
for n=1:3
regTxt{n}=sprintf('%s - %s',pairList{n,:});
end
hold on
pOrder=[2,1,3];
fprintf('in total, %0.2f %% of partical pairs are coupled\n',mean(dobFrac))
fprintf('\t %0.2f %% (%d/%d) of coupled pairs participated in triplets\n',mean([inTriple{:}])*100,sum([inTriple{:}]),sum(cellfun(@length,inTriple)))
temp=cat(1,inDouble{:});
fID=fopen('~/data/Fear/triple/analyses/paper/SourceData/fig06_d.csv','w');
sigText={'N.S.','Significant'};
fprintf(fID,'Fig. 6d\n\n')
for ii=1:3
tempPair=strrep(pairList(pOrder(ii),:),'PrL L','PL')
tempTxt=join(sigText(1+temp(:,pOrder(ii))),',');
fprintf(fID,'%s-%s,%s\n',tempPair{:},tempTxt{1})
end
fclose(fID)
for n=1:3
fprintf('%s : %0.2f %% of partical pairs are coupled\n',regTxt{pOrder(n)},dobFrac(1,pOrder(n)))
fprintf('\t %0.2f %% (%d/%d) of coupled pair are paericipating in triplets \n',inTriFrac(1,pOrder(n)),sum(inTriple{pOrder(n)}),length(inTriple{pOrder(n)}))
bar(n,dobFrac(1,pOrder(n)),0.8,'FaceColor',col(pOrder(n),:),'linestyle','none')
text(n,dobFrac(1,pOrder(n)),num2str(dobFrac(1,pOrder(n))),'FontSize',fs,'VerticalAlignment','top','HorizontalAlignment','center')
end
set(gca,'XTick',1:3,'XTickLabel',regTxt(pOrder),'XTickLabelRotation',-30)
ylabel({'Proportion of' 'coupled partial-pairs (%)'},'FontSize',fs,'FontWeight','normal')
colormap(gca,col)
box off
end
function panel_05(x,y,fs)
width=12;
height=16;
triple=poolVar('tripleAct.mat');
ses=poolVar('sessions.events.mat','base');
slp=poolVar('sleepstate.states.mat','base');
ratList=fieldnames(triple);
eachRate=[];
for ratIdx=1:length(ratList)
rat=ratList{ratIdx};
if isempty(triple.(rat).timestamps)
continue
end
rateTemp=[];
for hcIdx=1:2
slpTemp=relabel_ma2sleep(slp.(rat).MECE.timestamps);
slpTemp=slpTemp(slpTemp(:,2)>ses.(rat).homecage(hcIdx+1,1) & slpTemp(:,1)<ses.(rat).homecage(hcIdx+1,2),:);
if slpTemp(1,1)<ses.(rat).homecage(hcIdx+1,1); slpTemp(1,1)=ses.(rat).homecage(hcIdx+1,1);end
if slpTemp(end,2)>ses.(rat).homecage(hcIdx+1,2); slpTemp(end,2)=ses.(rat).homecage(hcIdx+1,2);end
behIdx=3;
target=slpTemp(slpTemp(:,3)==behIdx,1:2);
idxList=find(triple.(rat).isSig);
cnt=zeros(size(idxList));
for n=1:length(idxList)
idx=idxList(n);
cnt(n)=sum(any(triple.(rat).timestamps{idx}(:,3)>target(:,1)'& triple.(rat).timestamps{idx}(:,3)<target(:,2)',2));
end
rateTemp(:,hcIdx)=cnt/sum(diff(target,1,2))*60;
end
eachRate=[eachRate;rateTemp];
end
subplotInMM(x,y,width,height)
stateName={'wake','nrem','rem'};
col=setCoactColor;
behIdx=2;
hold on
fID=fopen('~/data/Fear/triple/analyses/paper/SourceData/fig06_e.csv','w');
fprintf(fID,'Fig. 6e\n\n');
fprintf(fID,'Pre-cond,%s\n',joinNumVec(eachRate(:,1)));
fprintf(fID,'Post-cond,%s\n',joinNumVec(eachRate(:,2)));
fclose(fID);
for n=1:2
bp=getBoxVal(eachRate(:,n));
if n==1
fc='w';
ls='-';
ec=col.triple;
lc=col.triple;
else
fc=col.triple;
ls='none';
ec=col.triple;
lc='w';
end
plot(n+[0,0],bp.minMax,'-','color',ec)
rectangle('Position',[n-0.25,bp.lower,0.5,bp.iqr],'EdgeColor',ec,'FaceColor',fc)
plot(n+0.25*[-1,1],bp.median+[0,0],'-','color',lc)
end
xticks(1:2)
xticklabels({'Pre-cond','Post-cond'})
xtickangle(-30)
title(upper({stateName{behIdx}}),'fontsize',fs,'fontweight','normal')
ylabel({'Triple-activation' 'event rate (1/min)'},'fontsize',fs)
xlim([0.25,2.75])
ylim([0,0.3])
yticks([0:0.1:0.3])
ax=fixAxis;
disp(['(n = ' num2str(size(eachRate,1)) ' triplets)'])
p=signrank(eachRate(:,1),eachRate(:,2));
if p <0.001
sigTxt='***';
elseif p<0.01
sigTxt='**';
elseif p<0.05
sigTxt='*';
else
sigTxt='';
end
text2(0.5,0.95,sigTxt,...
ax,'horizontalAlign','center')
end
function panel_06(x,y,fs)
width=24;
height=16;
yGap=15;
xGap=6;
ses=poolVar('sessions.events.mat','base');
slp=poolVar('sleepstate.states.mat','base');
rip=poolVar('ripples.events.mat','base');
hfo=poolVar('amyHfo.events.mat','base');
delta=poolVar('pfcSlowwave.new.events.mat','base');
ratList=fieldnames(rip);
triple=poolVar('tripleAct.mat');
pfcRip=poolVar('pfcGamma.events.mat','base');
smCore=normpdf(-4:4,0,1);
smCore=smCore/sum(smCore);
nWin=50;
binSize=0.02;
temp=[];
for ratIdx=1:length(ratList)
rat=ratList{ratIdx};
if isempty(triple.(rat).timestamps)
continue
end
if ~isfield(rip,rat)
continue
end
nrem=relabel_ma2sleep(slp.(rat).MECE.timestamps);
nrem=nrem(nrem(:,3)==3,1:2);
hcIdx=1;
nrem=nrem(nrem(:,2)>ses.(rat).homecage(1+hcIdx,1)&nrem(:,1)<ses.(rat).homecage(hcIdx+2,2),:);
hcIdx=1;
if nrem(1,1)<ses.(rat).homecage(hcIdx+1,1); nrem(1,1)=ses.(rat).homecage(hcIdx+1,1);end
hcIdx=2;
if nrem(end,2)>ses.(rat).homecage(hcIdx+1,2); nrem(end,2)=ses.(rat).homecage(hcIdx+1,2);end
subRip=rip.(rat).peaks.timestamps(any(rip.(rat).peaks.timestamps>nrem(:,1)' & rip.(rat).peaks.timestamps<nrem(:,2)',2));
subHfo=hfo.(rat).peaks.timestamps(any(hfo.(rat).peaks.timestamps>nrem(:,1)' & hfo.(rat).peaks.timestamps<nrem(:,2)',2));
[a,b]=find(abs(subRip-subHfo')<0.1);
coRip.(rat)=subRip(unique(a));
coHfo.(rat)=subHfo(unique(b));
end
for hcIdx=1:2
for evtType=1:5
eachPETH{hcIdx,evtType}=[];
eachCnt{hcIdx,evtType}=[];
end
end
for hcIdx=1:2
for ratIdx=1:length(ratList)
rat=ratList{ratIdx};
sigList=find(triple.(rat).isSig);
if isempty(sigList)
continue
end
nrem=relabel_ma2sleep(slp.(rat).MECE.timestamps);
nrem=nrem(nrem(:,3)==3,1:2);
nrem=nrem(nrem(:,1)>ses.(rat).homecage(hcIdx+1,1) & nrem(:,2)<ses.(rat).homecage(hcIdx+1,2),:);
triTime={};
for n=1:length(sigList)
idx=sigList(n);
eIdx=find(any(triple.hoegaarden181115.timestamps{idx}(:,3)>nrem(:,1)' &...
triple.hoegaarden181115.timestamps{idx}(:,3)<nrem(:,2)',2));
triTime{n}=triple.hoegaarden181115.timestamps{idx}(eIdx,:);
end
for evtType=1:5
switch evtType
case 1
evt=rip.(rat).peaks.timestamps;
evtName='SWR';
case 2
evt=hfo.(rat).peaks.timestamps;
evtName='HFO';
case 4
evt=delta.(rat).peak.timestamps;
evtName='slow-wave';
case 5
evt=coRip.(rat);
evtName='SWR-HFO';
case 3
evt=pfcRip.(rat)(4).peaks.timestamps;
evtName='pfcRip';
otherwise
continue
end
evt=evt(any(evt>nrem(:,1)'&evt<nrem(:,2)',2));
thisPETH=zeros(length(triTime),2*nWin+1,3);
thisCnt=zeros(length(triTime),2*nWin+1,3);
for tIdx=1:length(triTime)
for n=1:3
coT=triTime{tIdx}(:,n);
if isempty(coT)
thisPETH(tIdx,:,n)=0;
else
cnt=CCG([evt;coT],[ones(size(evt));2*ones(size(coT))],binSize,nWin,1);
thisPETH(tIdx,:,n)=conv(cnt(:,1,2)/length(evt)/binSize,smCore,'same');
thisCnt(tIdx,:,n)=cnt(:,1,2);
end
end
end
eachPETH{hcIdx,evtType}=[eachPETH{hcIdx,evtType};thisPETH];
eachCnt{hcIdx,evtType}=[eachCnt{hcIdx,evtType};thisCnt];
end
end
end
col=setCoactColor();
prePost={'Pre','Post'};
fID=fopen('~/data/Fear/triple/analyses/paper/SourceData/fig06_f.csv','w');
fprintf(fID,'Fig. 6f\n')
for evtType=1:4
switch evtType
case 1
evtName='SWR';
yRange=[0,0.3];
yTickPos=0:0.1:0.3;
rIdx=1;
regName='vCA1';
case 2
evtName='HFO';
yRange=[0,0.2];
yTickPos=0:0.1:0.2;
rIdx=2;
regName='BLA';
case 4
evtName='PL slow-wave';
yRange=[0,0.08];
yTickPos=0:0.04:0.08;
rIdx=3;