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compute_bsignif.m
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compute_bsignif.m
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%function compute_bsignif
%function compute_bsignif
% Compute burst significance from laminar data
%
% see also compute_tuning
%
% Corentin Massot
% Cognition and Sensorimotor Integration Lab, Neeraj J. Gandhi
% University of Pittsburgh
% created 06/23/2016 last modified 06/23/2017
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%set paths
[root_path data_path save_path]=set_paths;
%screen size
scrsz = get(groot,'ScreenSize');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%parameters
%print figures and save data
savedata=0;
savefigs=0;
figtype='epsc2';%'png';%'epsc2';
%alignement
%alignlist={'no' 'targ' 'go' 'sacc'};
%alignlist={'targ_pburst_ch' 'sacc' };
%alignlist={'targ_rsburst_ch' 'sacc' };
%alignlist={'targ_pburst_ch' 'targ_rsburst_ch'};
alignlist={'targ' 'sacc' };
%alignlist={'sacc' };
%windows of analysis
%plot
wind_targ=[-50 450];
wind_sacc=[-300 200];%[-200 200];
% %to compute bsignif
% %target 20deg
% wind_targ_bsignif=[100 200];
% wind_targ_bsl=[-50 50];
% wind_sacc_bsignif=[-25 75];
%
% %target 3deg
% wind_targ_bsignif=[100 150];
% wind_targ_bsl=[0 50];
% wind_sacc_bsignif=[-25 25];
%
% %wind_sacc_bsl=[-150 -100]
%vshift
vshift_spk=100;
%sigma FR
sigma_FR=6;
%burst trheshold
thresh=10;%threshold spk/s
%alpha test statistic
alpha=0.001
%thresholds for pburst constraints (just for display purposes, not involved in bsingif and thresh computation)
thresh_ratios=0.15;%0.15
thresh_surprises=4
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%get data
datalist=load_data_gandhilab(data_path);
%colorlist
colorlist=get_colorlist;
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%analyzing data
dlist=get_dlist
%hdlfigallbsignifs=figure;hold on;
data=[];
info=[];
for d=dlist%1:numel(datalist)
data=[];
%get data and info
info.datafile=datalist{d};
load ([data_path info.datafile]);
display(info.datafile)
%getting channel mapping and discard selected bad channels
[info.chmap info.nchannels info.depths]=get_chmap(data(1).info.electrode{2},[]);
%getting trial type
info.trialtype=data(1).sequence(1);
%getting list of targets
targslist=data(1).offline.targslist;
%targets index
targs_ind=get_targsindex(targslist,info);
targs_ind_flip=fliplr(targs_ind);
%target tuning (after compute_tuning)
targ_tuning=data(1).offline.targ_tuning;
%select trials
seltrials=get_seltrials(data,'rpt');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Compute size of adaptive window for analysis
% pos=targslist(targ_tuning,:);
% amp=sqrt(pos(1)^2+pos(2)^2);
% if amp>5,
% wadapt=floor(p(2)+amp*p(1));
% else
% wadapt=ceil(p(2)+5*p(1));
% end
wt=100;%50
wind_targ_bsignif=[110 110+wt];
wind_targ_bsl=[50-wt 50];
wind_targ_pburst=[0 wt];
wind_targ_pburst_bsl=[-50-wt -50 ];%[30-wt 30];
ws=50;
wind_sacc_bsignif=[25-ws 25];%[-25 -25+wadapt];
wind_sacc_bsl=[-150-ws -150];%[50-ws 50];%
wind_sacc_bsl_go=[-ws 0];%[50-ws 50];%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Data aligned on target and saccade onset
for al=1:numel(alignlist)
info.align=alignlist{al};
switch info.align
case 'targ'
[alltrials_spk_targ aligntime_targ]=get_alltrials_align(data,seltrials,wind_targ,'fr',info,targslist,sigma_FR,1);
%[alltrials_spk_targ_bsignif aligntime_targ_bsignif]=get_alltrials_align(data,seltrials,wind_targ_bsignif,'fr',info,targslist,sigma_FR,0);
[alltrials_spk_targ_bsignif aligntime_targ_bsignif]=get_alltrials_align(data,seltrials,wind_targ_bsignif,'fr',info,targslist,sigma_FR,0);
[alltrials_spk_targ_bsl aligntime_targ_bsl]=get_alltrials_align(data,seltrials,wind_targ_bsl,'fr',info,targslist,sigma_FR,0);
%bsl normalization
%[alltrials_spk_sacc_bsl aligntime_sacc_bsl]=get_alltrials_align(data,seltrials,wind_sacc_bsl,'fr',info,targslist,sigma_FR,0);
case 'targ_pburst_ch'
[alltrials_spk_targ aligntime_targ]=get_alltrials_align(data,seltrials,wind_targ,'fr',info,targslist,sigma_FR,1);
[alltrials_spk_targ_pburst aligntime_targ_pburst]=get_alltrials_align(data,seltrials,wind_targ_pburst,'fr',info,targslist,sigma_FR,0);
%alignaux=info.align;
%info.align='targ';
[alltrials_spk_targ_pburst_bsl aligntime_targ_pburst_bsl]=get_alltrials_align(data,seltrials,wind_targ_pburst_bsl,'fr',info,targslist,sigma_FR,0);
%info.align=alignaux;
case 'targ_rsburst_ch'
[alltrials_spk_targ aligntime_targ]=get_alltrials_align(data,seltrials,wind_targ,'fr',info,targslist,sigma_FR,1);
[alltrials_spk_targ_rsburst aligntime_targ_rsburst]=get_alltrials_align(data,seltrials,wind_targ_pburst,'fr',info,targslist,sigma_FR,0);
%alignaux=info.align;
%info.align='targ';
[alltrials_spk_targ_rsburst_bsl aligntime_targ_rsburst_bsl]=get_alltrials_align(data,seltrials,wind_targ_pburst_bsl,'fr',info,targslist,sigma_FR,0);
%info.align=alignaux;
case 'sacc'
[alltrials_spk_sacc aligntime_sacc]=get_alltrials_align(data,seltrials,wind_sacc,'fr',info,targslist,sigma_FR,1);
[alltrials_spk_sacc_bsignif aligntime_sacc_bsignif]=get_alltrials_align(data,seltrials,wind_sacc_bsignif,'fr',info,targslist,sigma_FR,0);
alignaux=info.align;
info.align='go';
[alltrials_spk_sacc_bsl aligntime_sacc_bsl]=get_alltrials_align(data,seltrials,wind_sacc_bsl_go,'fr',info,targslist,sigma_FR,0);
info.align=alignaux;
end
end
[allgazepos,allevents]=get_alldatagaze_align(data,seltrials,info,targslist);
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%target, target index and target in anti-RF
info.targ=targ_tuning;
info.targ_ind=find(targs_ind==targ_tuning);
targ_tuning_a=targs_ind_flip(info.targ_ind);
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%plot spk of targ and sacc
figbsignif=figure('Position',[1 100 scrsz(3)-100 scrsz(4)-200]);
for al=1:numel(alignlist)
info.align=alignlist{al};
switch info.align
case 'targ'
info.aligntime=aligntime_targ;
wind_bsignif=wind_targ_bsignif;
trials_spk=alltrials_spk_targ{targ_tuning};
wind_bsl=wind_targ_bsl;
trials_spk_bsl=alltrials_spk_targ_bsl{targ_tuning};
case 'targ_pburst_ch'
info.aligntime=aligntime_targ_pburst;
wind_bsignif=wind_targ_pburst;
trials_spk=alltrials_spk_targ_pburst{targ_tuning};
wind_bsl=wind_targ_pburst_bsl;
trials_spk_bsl=alltrials_spk_targ_pburst_bsl{targ_tuning};
case 'targ_rsburst_ch'
info.aligntime=aligntime_targ_rsburst;
wind_bsignif=wind_targ_pburst;
trials_spk=alltrials_spk_targ_rsburst{targ_tuning};
wind_bsl=wind_targ_pburst_bsl;
trials_spk_bsl=alltrials_spk_targ_rsburst_bsl{targ_tuning};
case 'sacc'
info.aligntime=aligntime_sacc;
wind_bsignif=wind_sacc_bsignif;
trials_spk=alltrials_spk_sacc{targ_tuning};
wind_bsl=wind_sacc_bsl;
trials_spk_bsl=alltrials_spk_sacc_bsl{targ_tuning};
end
gazepos=allgazepos{info.targ};
events=allevents{info.targ};
%%baseline
%wind_bsl=wind_targ_bsl;
%trials_spk_bsl=alltrials_spk_targ_bsl{targ_tuning};
[info.nchannels info.ntrials info.triallen]=size(trials_spk);
%compute average trials
[trials_spk_avg trials_spk_var]=get_trials_avg(trials_spk);
%remove trials with amplitude that is too small
%[trials_spk_avgc index_spk_c]=clean_trials(trials_spk_avg,'fr');
%compute average trials of baseline
[trials_spk_bsl_avg trials_spk_bsl_var]=get_trials_avg(trials_spk_bsl);
%normalize average trials by baseline
%trials_spk_avgcn=get_trials_normalized(trials_spk_avgc,trials_spk_bsl_avg,'fr',info);
trials_spk_avgn=get_trials_avg_normalized(trials_spk_avg,trials_spk_bsl_avg,'fr',info);
%plot
hdlfig=subplot(1,2,al);hold on;
titlestr={info.datafile ; ['FR ' info.align ' t' num2str(info.targ) ' #trials:' num2str(info.ntrials)]};
[range ~]=plot_trials(trials_spk_avgn,[],[1:info.nchannels],vshift_spk,[],[],info,hdlfig,titlestr,[],[]);
%plot wind_bsignif limits
plot_event(wind_bsignif,info.aligntime,range,1,hdlfig);
%plot wind_bsl limits
%if strcmp(info.align,'targ')
plot_event(wind_bsl,info.aligntime,range,3,hdlfig);
%end
%same axis
if al==1,
axis tight;
ax1=axis;
else
axis tight;
ax2=axis;
axis([ax2(1) ax2(2) ax1(3) ax1(4)]);
end
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %Update data thresh_al
% %thresh=5;%threshold spk/s
% thresh_al=mean(trials_spk_avgn,2)>thresh; %select channel when at any time the mean FR crossed the threshold
% %pause
% data=update_data(0,1,0,data,data_path,info.datafile,field,thresh_al);
end
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%compute threshold of targ and sacc
%TODO: fix plot of targ signals
figthresh=figure('Position',[1 100 scrsz(3)-100 scrsz(4)-200]);
for al=1:numel(alignlist)
info.align=alignlist{al};
switch info.align
case 'targ'
info.aligntime=aligntime_targ_bsignif;
wind_bsignif=wind_targ_bsignif;
trials_spk=alltrials_spk_targ_bsignif{targ_tuning};
wind_bsl=wind_targ_bsl;
trials_spk_bsl=alltrials_spk_targ_bsl{targ_tuning};
field='targ_bthresh';
case 'targ_pburst_ch'
info.aligntime=aligntime_targ_pburst;
wind_bsignif=wind_targ_pburst;
trials_spk=alltrials_spk_targ_pburst{targ_tuning};
wind_bsl=wind_targ_pburst_bsl;
trials_spk_bsl=alltrials_spk_targ_pburst_bsl{targ_tuning};
field='targ_pburstch_bthresh';
case 'targ_rsburst_ch'
info.aligntime=aligntime_targ_rsburst;
wind_bsignif=wind_targ_pburst;
trials_spk=alltrials_spk_targ_rsburst{targ_tuning};
wind_bsl=wind_targ_pburst_bsl;
trials_spk_bsl=alltrials_spk_targ_rsburst_bsl{targ_tuning};
field='targ_rsburstch_bthresh';
case 'sacc'
info.aligntime=aligntime_sacc_bsignif;
wind_bsignif=wind_sacc_bsignif;
trials_spk=alltrials_spk_sacc_bsignif{targ_tuning};
wind_bsl=wind_sacc_bsl;
trials_spk_bsl=alltrials_spk_sacc_bsl{targ_tuning};
field='sacc_bthresh';
end
gazepos=allgazepos{info.targ};
events=allevents{info.targ};
%%baseline
%wind_bsl=wind_targ_bsl;
%trials_spk_bsl=alltrials_spk_targ_bsl{targ_tuning};
[info.nchannels info.ntrials info.triallen]=size(trials_spk);
%normalization of each trial
trials_spk_n=get_trials_normalized(trials_spk,trials_spk_bsl,'FR',info);
%compute average trials
[trials_spk_avg trials_spk_var]=get_trials_avg(trials_spk);
%remove trials with amplitude that is too small
%[trials_spk_avgc index_spk_c]=clean_trials(trials_spk_avg,'fr');
%compute average trials of baseline
[trials_spk_bsl_avg trials_spk_bsl_var]=get_trials_avg(trials_spk_bsl);
%normalize average trials by baseline
%trials_spk_avgcn=get_trials_normalized(trials_spk_avgc,trials_spk_bsl_avg,'fr',info);
trials_spk_avgn=get_trials_avg_normalized(trials_spk_avg,trials_spk_bsl_avg,'fr',info);
%plot
hdlfig=subplot(1,2,al);hold on;
titlestr={info.datafile ; ['FR ' info.align ' t' num2str(info.targ) ' #trials:' num2str(info.ntrials)]};
[range ~]=plot_trials(trials_spk_avgn,[],[1:info.nchannels],vshift_spk,[],[],info,hdlfig,titlestr,[],[]);
%plot wind_bsignif limits
plot_event(wind_bsignif,info.aligntime,range,1,hdlfig);
%plot wind_bsl limits
%if strcmp(info.align,'targ')
plot_event(wind_bsl,info.aligntime,range,3,hdlfig);
%end
%same axis
if al==1,
axis tight;
ax1=axis;
else
axis tight;
ax2=axis;
axis([ax2(1) ax2(2) ax1(3) ax1(4)]);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Update data thresh_al
%thresh_al_trials
%thresh_al_trials=nanmedian(mean(trials_spk_n,[],3),2)>thresh;
thresh_al_trials=nanmedian(mean(trials_spk_n,3),2)>thresh;
data=update_data(0,1,0,data,data_path,info.datafile,[field '_trials'],thresh_al_trials);
%thresh_al
%thresh_al=mean(trials_spk_avgn,[],2)>thresh; %select channel when at any time the mean FR crossed the threshold
thresh_al=mean(trials_spk_avgn,2)>thresh; %select channel when at any time the mean FR crossed the threshold
data=update_data(0,1,0,data,data_path,info.datafile,field,thresh_al);
%pause
end
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%compute significance of burst of activity for the different alignements
figure(figbsignif);
for al=1:numel(alignlist)
info.align=alignlist{al};
switch info.align
case 'targ'
field='targ_bsignif';
wind_bsignif=wind_targ_bsignif;
info.aligntime=aligntime_targ;
%in RF
trials_spk_bsignif=alltrials_spk_targ_bsignif{targ_tuning};
trials_spk_bsl=alltrials_spk_targ_bsl{targ_tuning};
%in anti-RF
trials_spk_bsignif_a=alltrials_spk_targ_bsignif{targ_tuning_a};
trials_spk_bsl_a=alltrials_spk_targ_bsl{targ_tuning_a};
%thesh_al
%thresh_al=data(1).offline.targ_bthresh;
thresh_al=data(1).offline.targ_bthresh_trials;
case 'targ_pburst_ch'
field='targ_pburstch_bsignif';
wind_bsignif=wind_targ_pburst;
info.aligntime=aligntime_targ_pburst;
%in RF
trials_spk_bsignif=alltrials_spk_targ_pburst{targ_tuning};
trials_spk_bsl=alltrials_spk_targ_pburst_bsl{targ_tuning};
%in anti-RF
trials_spk_bsignif_a=alltrials_spk_targ_pburst{targ_tuning_a};
trials_spk_bsl_a=alltrials_spk_targ_pburst_bsl{targ_tuning_a};
%thesh_al
%thresh_al=data(1).offline.targ_pburstch_bthresh;
thresh_al=data(1).offline.targ_pburstch_bthresh_trials;
case 'targ_rsburst_ch'
field='targ_rsburstch_bsignif';
wind_bsignif=wind_targ_pburst;
info.aligntime=aligntime_targ_rsburst;
%in RF
trials_spk_bsignif=alltrials_spk_targ_rsburst{targ_tuning};
trials_spk_bsl=alltrials_spk_targ_rsburst_bsl{targ_tuning};
%in anti-RF
trials_spk_bsignif_a=alltrials_spk_targ_rsburst{targ_tuning_a};
trials_spk_bsl_a=alltrials_spk_targ_rsburst_bsl{targ_tuning_a};
%thesh_al
%thresh_al=data(1).offline.targ_rsburstch_bthresh;
thresh_al=data(1).offline.targ_rsburstch_bthresh_trials;
case 'sacc'
field='sacc_bsignif';
wind_bsignif=wind_sacc_bsignif;
info.aligntime=aligntime_sacc;
%in RF
trials_spk_bsignif=alltrials_spk_sacc_bsignif{targ_tuning};
trials_spk_bsl=alltrials_spk_sacc_bsl{targ_tuning};
%in anti-RF
trials_spk_bsignif_a=alltrials_spk_sacc_bsignif{targ_tuning_a};
trials_spk_bsl_a=alltrials_spk_sacc_bsl{targ_tuning_a};
%thesh_al
%thresh_al=data(1).offline.sacc_bthresh;
thresh_al=data(1).offline.sacc_bthresh_trials;
end
%%baseline
%trials_spk_bsl={targ_tuning};
%trials_spk_bsl_a=alltrials_spk_targ_bsl{targ_tuning_a};
%Peak significance
%compare to baseline
H_al=get_bsignif(trials_spk_bsignif,trials_spk_bsl,[],[],alpha);
%compare to anti-RF (NOTE not good because sometime clear burst and not selected)
%H_al=get_bsignif(trials_spk_bsignif,trials_spk_bsignif_a,trials_spk_bsl,trials_spk_bsl_a,0.01);
%plot bsignif
hdlfig=subplot(1,2,al);hold on;
center_bsignif(:,1)=H_al'.*(round(wind_bsignif(2)-wind_bsignif(1))/2+wind_bsignif(1)+1*[1:info.nchannels]');
center_bsignif(find(center_bsignif(:,1)==0),1)=-info.aligntime;
center_bsignif(:,2)=0;%vshift_spk;
plot_events_ch(center_bsignif,[],vshift_spk,range,info,hdlfig,[],'-',2,'');
% %plot thresh_al
% hdlfig=subplot(1,2,al);hold on;
% center_bsignif(:,1)=(thresh_al).*(round(wind_bsignif(2)-wind_bsignif(1))/2+wind_bsignif(1)+5+1*[1:info.nchannels]');
% center_bsignif(find(center_bsignif(:,1)==0),1)=-info.aligntime;
% center_bsignif(:,2)=0;%vshift_spk;
% plot_events_ch(center_bsignif,[],vshift_spk,range,info,hdlfig,[],'-.',2);
%plot thresh_al_trials
hdlfig=subplot(1,2,al);hold on;
center_bsignif(:,1)=(thresh_al_trials).*(round(wind_bsignif(2)-wind_bsignif(1))/2+wind_bsignif(1)+5+1*[1:info.nchannels]');
center_bsignif(find(center_bsignif(:,1)==0),1)=-info.aligntime;
center_bsignif(:,2)=0;%vshift_spk;
plot_events_ch(center_bsignif,[],vshift_spk,range,info,hdlfig,[],'-.',2,'');
%%
%plot pburst_signif
switch info.align
case 'targ_pburst_ch'
ratios=data(1).offline.targ_pburst_ratio(targ_tuning,:)>thresh_ratios;
surprises=data(1).offline.targ_pburst_msurprises(targ_tuning,:)>thresh_surprises;
case 'targ_rsburst_ch'
ratios=data(1).offline.targ_rsburst_ratio(targ_tuning,:)>thresh_ratios;
surprises=data(1).offline.targ_rsburst_msurprises(targ_tuning,:)>thresh_surprises;
case 'sacc'
ratios=data(1).offline.sacc_pburst_ratio(targ_tuning,:)>thresh_ratios;
surprises=data(1).offline.sacc_pburst_msurprises(targ_tuning,:)>thresh_surprises;
end
pburst_signif=[];
pburst_signif=(ratios & surprises)';
hdlfig=subplot(1,2,al);hold on;
center_bsignif(:,1)=(pburst_signif).*(round(wind_bsignif(2)-wind_bsignif(1))/2+wind_bsignif(1)+15+1*[1:info.nchannels]');
center_bsignif(find(center_bsignif(:,1)==0),1)=-info.aligntime;
center_bsignif(:,2)=0;%vshift_spk;
plot_events_ch(center_bsignif,[],vshift_spk,range,info,hdlfig,[],'-',2,'');
%Update data H_al
data=update_data(0,1,0,data,data_path,info.datafile,field,H_al);
end
%data(1).offline.targ_bsignif
%data(1).offline.sacc_bsignif
%%
%update data
%display('NOT SAVED!')
update_data(1,0,0,data,data_path,info.datafile,[],[]);
%pause
close(figbsignif)
close(figthresh)
end