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SpikingReproducibility.m
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%%%%%%%%%
% re-saving 'batchbatchFANOionto' as 'SpikingReproducibility'
% and cleaning up the plotting and analyses parts
%%%%%%%%%%%%%
% cd /Users/kperks/GitHub/iontoncm/B444/Left_R-300_L1000/Z1230/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B444/Left_R-300_L1000/Z1460/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B444/Left_R-300_L1000/Z1590/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B444/Left_R-300_L1000/Z1810/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B444/Left_R-300_L1000/Z2570/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B444/Left_R-300_L1000/Z2680/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B444/Left_R-300_L1000/Z3200/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B444/Left_R-500_L1000/Z2000/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B444/Left_R-500_L1000/Z2450/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
base_data_All = [];
gz_data_All = [];
cd /Users/kperks/GitHub/iontoncm/B445/Left_R-200_L1000/Z1550/ss001
[base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,0);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
% [base_data, gz_data] = batchFANOionto(start,stop,blocksize,blocktype,sitetype,smooth,doprintout)
cd /Users/kperks/GitHub/iontoncm/B445/Left_R-200_L1000/Z1670/ss001
[base_data2, gz_data2] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B445/Left_R-200_L1000/Z1750/ss001
[base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B445/Left_R-200_L1000/Z1860/ss001
[base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B445/Left_R-200_L1000/Z2150/ss001
[base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B445/Left_R-200_L1000/Z2330/ss001
[base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B445/Left_R-200_L1000/Z2770/ss001
[base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z1000/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z1055/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'su',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z1151/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z1260/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'su',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z1330/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'su',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z1440/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z1480/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z1570/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z1700/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'su',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z2650/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'su',0,1)
% % cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z780/ss001
% % batchrasterionto2
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z920/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,5,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z950/ss003
% [base_data, gz_data] = batchFANOionto(-2,12,5,[1 2 5],'su',0,1)
% cd /Users/kperks/GitHub/iontoncm/B493/Right_R-350_L1100/Z950/ss004
% [base_data, gz_data] = batchFANOionto(-2,12,5,[1 2 5],'su',0,1)
%
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z1110/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z1150/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z1260/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z1310/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z1440/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z1520/ss003
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z1640/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z1760/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z2190/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z2250/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'su',0,1)
% cd /Users/kperks/GitHub/iontoncm/B484/Left_R-300_L1000/Z1370/ss001
% [base_data, gz_data] = batchFANOionto(-2,12,10,[1 2 5],'mu',0,1)
cd /Users/kperks/GitHub/iontoncm/B450/Right_R-300_L1000/Z830/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B450/Right_R-300_L1000/Z2040/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B450/Right_R-300_L1000/Z2100/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B450/Right_R-300_L1000/Z2250/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B450/Right_R-300_L1000/Z2350/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B450/Right_R-300_L1000/Z2480/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 3 5],'su',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B450/Right_R-300_L1000/Z2600/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'su',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B450/Right_R-300_L1000/Z2800/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B466/Left_R-200_L1000/Z780/ss002/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 4 24 5 3 23 5],'su',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B466/Left_R-200_L1000/Z2150/ss002/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 4 24 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B466/Left_R-200_L1000/Z2210/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 4 24 5 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B466/Left_R-200_L1000/Z2250/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B466/Left_R-200_L1000/Z2311/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 4 24 5],'su',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B466/Left_R-200_L1000/Z2430/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 4 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B466/Left_R-350_L1000/Z2800/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5 4 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B466/Left_R-350_L1000/Z2880/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'su',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B504/LEFT_R-300_L1000/Z660/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 24 5 3 5],'su',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B504/LEFT_R-300_L1000/Z660/ss002/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 24 5 3 5],'su',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B504/LEFT_R-300_L1000/Z2150/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 24 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B504/LEFT_R-300_L1000/Z2280/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 24 5 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B504/LEFT_R-300_L1000/Z2430/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B504/LEFT_R-300_L1000/Z2650/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 24 5],'su',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B504/LEFT_R-300_L1000/Z2810/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B504/LEFT_R-300_L1000/Z2910/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B504/LEFT_R-300_L1000/Z2990/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'su',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B504/LEFT_R-300_L1000/Z3032/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B490/Right_R-300_L1000/Z970/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 24 5 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B490/Right_R-300_L1000/Z1170/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 24 5 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B490/Right_R-300_L1000/Z1461/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B490/Right_R-300_L1000/Z1570/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B490/Right_R-300_L1000/Z1850/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B490/Right_R-300_L1000/Z2101/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B490/Right_R-300_L1000/Z2220/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 5],'su',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B490/Right_R-300_L1000/Z2620/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 24 5 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
cd /Users/kperks/GitHub/iontoncm/B490/Right_R-300_L1000/Z2811/ss001/
[base_data, gz_data] = batchFANOionto(-2,7,10,[1 2 24 5 3 5],'mu',0,1);
base_data_All = [base_data_All base_data];
gz_data_All = [gz_data_All gz_data];
%%
meanspks = [];
tmpspks = [];
trial_len = [];
spkvec = [];
for icond = 1:max(size(base_data_All))
tmpspks = zeros(size(base_data_All(icond).spikes,1),size(base_data_All(icond).spikes,2));
for itrial = 1:size(base_data_All(icond).spikes,1)
tmpspks(itrial,find(base_data_All(icond).spikes(itrial,:))) = 1;
end
trial_len(icond) = size(base_data_All(icond).spikes,2);
meanspks{icond} = mean(tmpspks);
end
for icond = 1:max(size(base_data_All))
spkvec(icond,:) = meanspks{icond}(1,1:min(trial_len));
end
%% set up params
times = 25:50:size(tmp_pre,2)-24; % from 1950 ms before target onset until 2000 ms after.
fanoParams.alignTime = size(tmp_pre,2)/2; % this time will become zero time fanoParams.boxWidth = 50; % 50 ms sliding window.
fanoParams.matchReps = 10;
fanoParams.binSpacing = 0.25;
fanoParams.boxWidth = boxWidth;
%% split and combine gz and base data
% to get pre and post stim array that has
% base as first half and gz for second half of split for Fano anal
start_stim = 2000;
boxWidth = 50;
data_len = (boxWidth * floor((start_stim - 1)/50));
pre_data = [];
post_data = [];
tmp_post = [];
tmp_pre = [];
for iar = 1:size(gz_data_All,2)
this_ar_gz = gz_data_All(iar).spikes;
this_ar_bs = base_data_All(iar).spikes;
for itrial = 1:size(this_ar_gz,1)
prestart = (start_stim - 1) - data_len;
tmp_pre(itrial,:) = [this_ar_bs(itrial,prestart:(start_stim - 1)) ...
this_ar_gz(itrial,prestart:(start_stim - 1)) ];
postend = (start_stim + 50) + data_len;
tmp_post(itrial,:) = [this_ar_bs(itrial,(start_stim + 50):4000) ...
this_ar_gz(itrial,(start_stim + 50):4000) ];
end
pre_data(iar).spikes = tmp_pre;
post_data(iar).spikes = tmp_post;
end
%%
%%%%%%%%%%%%%%%
%for gaba condition...
times = 25:50:size(tmp_pre,2)-24; % from 1950 ms before target onset until 2000 ms after.
fanoParams.alignTime = (size(tmp_pre,2)/2)-25; % this time will become zero time fanoParams.boxWidth = 50; % 50 ms sliding window.
fanoParams.matchReps = 10;
fanoParams.binSpacing = 0.25;
fanoParams.boxWidth = boxWidth;
Result_pre = VarVsMean(pre_data, times, fanoParams);
plotFano(Result_pre);
hfig = figure;hold on
subplot(4,1,1)
hold on
data_split = size(Result_pre.meanRateAll,1)/2;
plot(Result_pre.meanRateSelect(1:data_split),'color','k','LineWidth',3)
plot(Result_pre.meanRateSelect(data_split + 1 :end),'color','r','LineWidth',3)
axis tight
ylabel('mean count Raw','FontSize',16)
subplot(4,1,2);hold on
plot(Result_pre.FanoFactor(1:data_split),'color','k','LineWidth',3)
plot(Result_pre.FanoFactor(data_split + 1 :end),'color','r','LineWidth',3)
axis tight
ylabel('FanoFactor matched','FontSize',16)
subplot(4,1,3);hold on
range = max(Result_pre.FanoFactor)-min(Result_pre.FanoFactor);
bins = (range / 10);
edges = [min(Result_pre.FanoFactor):bins:max(Result_pre.FanoFactor)];
bins_b = histc(Result_pre.FanoFactor(1:data_split),edges)./data_split;
bins_i = histc(Result_pre.FanoFactor(data_split + 1 :end),edges)./data_split;
line(edges,bins_b,'color','k','LineWidth',3)
line(edges,bins_i,'color','r','LineWidth',3)
ylabel('p(FF)','FontSize',16)
kstest2(Result_pre.FanoFactor(1:data_split),Result_pre.FanoFactor(data_split + 1 :end))
subplot(4,1,4);hold on
FF = [(Result_pre.FanoFactor + Result_pre.Fano_95CIs(:,1)); ...
(Result_pre.FanoFactor + Result_pre.Fano_95CIs(:,2))];
range = max(FF)-min(FF);
bins = (range / 10);
edges = [min(FF):bins:max(FF)];
FF_b = [(Result_pre.FanoFactor(1:data_split,1) + Result_pre.Fano_95CIs(1:data_split,1)); ...
(Result_pre.FanoFactor(1:data_split,1) + Result_pre.Fano_95CIs(1:data_split,2))];
bins_b = histc(FF_b,edges)./size(FF_b,1);
FF_i = [(Result_pre.FanoFactor(data_split + 1 :end,1) + Result_pre.Fano_95CIs(data_split + 1 :end,1)); ...
(Result_pre.FanoFactor(data_split + 1 :end,1) + Result_pre.Fano_95CIs(data_split + 1 :end,2))];
bins_i = histc(FF_i,edges)./size(FF_i,1);
line(edges,bins_b,'color','k','LineWidth',3)
line(edges,bins_i,'color','r','LineWidth',3)
ylabel('p(FF) : 95%CI added','FontSize',16)
FF_b = Result_pre.FanoFactor(1:data_split);
FF_i = Result_pre.FanoFactor(data_split + 1 :end);
[h,p] = kstest2(FF_b,FF_i)
intact_prestim_FF = median(FF_b)
CI = getCDFconf(FF_b,95)
gaba_prestim_FF = median(FF_i)
CI = getCDFconf(FF_b,95)
set(hfig,'Position',[440 92 487 706]);
%%%%%%%%%%%%%%%
%for intact condition...
% times = 25:50:size(tmp_post,2)-24; % from 1950 ms before target onset until 2000 ms after.
% fanoParams.alignTime = (size(tmp_post,2)/2)-25; % this time will become zero time fanoParams.boxWidth = 50; % 50 ms sliding window.
% fanoParams.matchReps = 10;
% fanoParams.binSpacing = 0.25;
% fanoParams.boxWidth = 50;
Result_post = VarVsMean(post_data, times, fanoParams);
plotFano(Result_post);
hfig = figure;hold on
subplot(4,1,1)
hold on
data_split = size(Result_post.meanRateAll,1)/2;
% plot(Result_post.meanRateAll(1:data_split),'--.k','LineWidth',2)
% plot(Result_post.meanRateAll(data_split + 1 :end),'--.r','LineWidth',2)
plot(Result_post.meanRateSelect(1:data_split),'color','k','LineWidth',3)
plot(Result_post.meanRateSelect(data_split + 1 :end),'color','r','LineWidth',3)
axis tight
ylabel('mean count Raw','FontSize',16)
subplot(4,1,2);hold on
% plot(Result_post.FanoFactorAll(1:data_split),'--.k','LineWidth',2)
% plot(Result_post.FanoFactorAll(data_split + 1 :end),'--.r','LineWidth',2)
plot(Result_post.FanoFactor(1:data_split),'color','k','LineWidth',3)
plot(Result_post.FanoFactor(data_split + 1 :end),'color','r','LineWidth',3)
axis tight
ylabel('FanoFactor matched','FontSize',16)
subplot(4,1,3);hold on
range = max(Result_post.FanoFactor)-min(Result_post.FanoFactor);
bins = (range / 10);
edges = [min(Result_post.FanoFactor):bins:max(Result_post.FanoFactor)];
bins_b = histc(Result_post.FanoFactor(1:data_split),edges)./data_split;
bins_i = histc(Result_post.FanoFactor(data_split + 1 :end),edges)./data_split;
line(edges,bins_b,'color','k','LineWidth',3)
line(edges,bins_i,'color','r','LineWidth',3)
ylabel('p(FF)','FontSize',16)
kstest2(Result_post.FanoFactor(1:data_split),Result_post.FanoFactor(data_split + 1 :end))
subplot(4,1,4);hold on
FF = [(Result_post.FanoFactor + Result_post.Fano_95CIs(:,1)); ...
(Result_post.FanoFactor + Result_post.Fano_95CIs(:,2))];
range = max(FF)-min(FF);
bins = (range / 10);
edges = [min(FF):bins:max(FF)];
FF_b = [(Result_post.FanoFactor(1:data_split,1) + Result_post.Fano_95CIs(1:data_split,1)); ...
(Result_post.FanoFactor(1:data_split,1) + Result_post.Fano_95CIs(1:data_split,2))];
bins_b = histc(FF_b,edges)./size(FF_b,1);
FF_i = [(Result_post.FanoFactor(data_split + 1 :end,1) + Result_post.Fano_95CIs(data_split + 1 :end,1)); ...
(Result_post.FanoFactor(data_split + 1 :end,1) + Result_post.Fano_95CIs(data_split + 1 :end,2))];
bins_i = histc(FF_i,edges)./size(FF_i,1);
line(edges,bins_b,'color','k','LineWidth',3)
line(edges,bins_i,'color','r','LineWidth',3)
ylabel('p(FF) : 95%CI added','FontSize',16)
set(hfig,'Position',[440 92 487 706]);
FF_b = Result_post.FanoFactor(1:data_split);
FF_i = Result_post.FanoFactor(data_split + 1 :end);
[h,p] = kstest2(FF_b,FF_i)
intact_stimulus_FF = median(FF_b)
CI = getCDFconf(FF_b,95)
gaba_stimulus_FF = median(FF_i)
CI = getCDFconf(FF_i,95)
%%
%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% start here to plot normalized onset and offset and fitlines
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if highres ==1;
boxW = 20;
%%%%%%%%%%%%%%
%get offset data
zerotime = 7000;
%used aligned spikes trains so that end is at beginning
for icond = 1:size(base_data_All,2)
condlen = size(base_data_All(icond).spikes,2);
condend = condlen - zerotime + 2000 - 1;
lastbit(icond).spikes = base_data_All(icond).spikes(:,(condend):end);
lastbit_gz(icond).spikes = gz_data_All(icond).spikes(:,(condend):end);
end
times = (zerotime-4000)+boxW/2:boxW/2:(8999-boxW); % from 4000 ms before target offset until 2000 ms after.
fanoParams.alignTime = zerotime-(boxW/2); % this time will become zero time fanoParams.boxWidth = 50; % 50 ms sliding window.
fanoParams.matchReps = 10;
fanoParams.binSpacing = 0.25;
fanoParams.boxWidth = boxW;
Result_base_end = VarVsMean(lastbit, times, fanoParams);
% plotFano(Result_base_end);
Result_gz_end = VarVsMean(lastbit_gz, times, fanoParams);
% plotFano(Result_gz_end);
figure;hold on
line(Result_base_end.times,Result_base_end.meanRateAll,'color','k')
line(Result_gz_end.times,Result_gz_end.meanRateAll,'color','r')
set(gca,'XLim',[-1000,1500])
figure;hold on
line(Result_base_end.times,Result_base_end.FanoFactorAll,'color','k')
line(Result_gz_end.times,Result_gz_end.FanoFactorAll,'color','r')
%%%%%%%%%%%%%%%%
%get onset data
zerotime = 2000;
times = boxW/2:boxW/2:zerotime + 4000 - boxW/2; % from 1950 ms before target onset until 2000 ms after.
fanoParams.alignTime = zerotime - (boxW/2); % this time will become zero time fanoParams.boxWidth = 50; % 50 ms sliding window.
fanoParams.matchReps = 10;
fanoParams.binSpacing = 0.25;
fanoParams.boxWidth = boxW;
Result_base = VarVsMean(base_data_All, times, fanoParams);
% plotFano(Result_base);
Result_gz = VarVsMean(gz_data_All, times, fanoParams);
% plotFano(Result_gz);
figure;hold on
line(Result_base.times,Result_base.meanRateAll,'color','k')
line(Result_gz.times,Result_gz.meanRateAll,'color','r')
axis tight
figure;hold on
plot(Result_base.times,Result_base.FanoFactor,'color','k')
plot(Result_base.times,Result_gz.FanoFactor,'color','r')
axis tight
end
if highres ==0
%%%%%%%%%%%%%%
%get offset data
%used aligned spikes trains so that end is at beginning
for icond = 1:size(base_data_All,2)
condlen = size(base_data_All(icond).spikes,2);
condend = condlen - 8999;
lastbit(icond).spikes = base_data_All(icond).spikes(:,(condend):end);
lastbit_gz(icond).spikes = gz_data_All(icond).spikes(:,(condend):end);
end
times = 3025:50:8950; % from 5000 ms before target onset until 2000 ms after.
fanoParams.alignTime = 6975; % this time will become zero time fanoParams.boxWidth = 50; % 50 ms sliding window.
fanoParams.matchReps = 10;
fanoParams.binSpacing = 0.25;
fanoParams.boxWidth = 50;
Result_base_end = VarVsMean(lastbit, times, fanoParams);
% plotFano(Result_base_end);
Result_gz_end = VarVsMean(lastbit_gz, times, fanoParams);
% plotFano(Result_gz_end);
figure;hold on
line(Result_base_end.times,Result_base_end.meanRateAll,'color','k')
line(Result_gz_end.times,Result_gz_end.meanRateAll,'color','r')
set(gca,'XLim',[-1000,1500])
figure;hold on
line(Result_base_end.times,Result_base_end.FanoFactorAll,'color','k')
line(Result_gz_end.times,Result_gz_end.FanoFactorAll,'color','r')
%%%%%%%%%%%%%%%%
%get onset data
times = 25:50:6000; % from 1950 ms before target onset until 2000 ms after.
fanoParams.alignTime = 1975; % this time will become zero time fanoParams.boxWidth = 50; % 50 ms sliding window.
fanoParams.matchReps = 10;
fanoParams.binSpacing = 0.25;
fanoParams.boxWidth = 50;
Result_base = VarVsMean(base_data_All, times, fanoParams);
% plotFano(Result_base);
Result_gz = VarVsMean(gz_data_All, times, fanoParams);
% plotFano(Result_gz);
figure;hold on
line(Result_base.times,Result_base.meanRateAll,'color','k')
line(Result_gz.times,Result_gz.meanRateAll,'color','r')
axis tight
figure;hold on
plot(Result_base.times,Result_base.FanoFactor,'color','k')
plot(Result_base.times,Result_gz.FanoFactor,'color','r')
axis tight
end
%%%%%%%%%%%%%%%
% plot onset and offset as function of pre-stim FF
% onset as a % of mean baseline FF and quantify
onsetind = max(find(Result_base.times <= 0));
prestimFF_base = mean(Result_base.FanoFactor(1:onsetind));
prestimFF_gz = mean(Result_gz.FanoFactor(1:onsetind));
norm_base = Result_base.FanoFactor / prestimFF_base;
norm_base_CI = Result_base.Fano_95CIs / prestimFF_base;
meanDropFF_base = mean(norm_base(onsetind+5:end));
norm_gaba = Result_gz.FanoFactor / prestimFF_gz;
norm_gaba_CI = Result_gz.Fano_95CIs/ prestimFF_gz;
meanDropFF_gaba = mean(norm_gaba(onsetind+5:end));
% offset as a % pre-stim mean baseline FF
offsetind = max(find(Result_base_end.times < 0));
norm_base_end = Result_base_end.FanoFactor / prestimFF_base;
norm_base_CI_end = Result_base_end.Fano_95CIs / prestimFF_base;
meanDropFFend_base = mean(norm_base_end(5:offsetind-5));
norm_gaba_end = Result_gz_end.FanoFactor / prestimFF_gz;
norm_gaba_CI_end = Result_gz_end.Fano_95CIs / prestimFF_gz;
meanDropFFend_gaba = mean(norm_gaba_end(5:offsetind-5));
avgdrop_base = mean([meanDropFF_base,meanDropFFend_base])
avgdrop_gz = mean([meanDropFF_gaba,meanDropFFend_gaba])
% Fano in intact condition aligned at on and off
%also get mean Fano relative to baseline and CI
hfig = figure;
hold on
onsetT = Result_base.times;
clipend = find(Result_base.times == 2000);
offsetT = Result_base_end.times + size(Result_base.times,1)*fanoParams.boxWidth;
clipon = find(Result_base_end.times == -2000);
line(onsetT(1:clipend),norm_base(1:clipend),'color','k','LineWidth',2)
line(offsetT(clipon:end),norm_base_end(clipon:end),'color','k','LineWidth',2)
% line(onsetT(1:clipend),norm_gaba(1:clipend),'color','r')
% line(offsetT(clipon:end),norm_gaba_end(clipon:end),'color','r')
line([0,0],[0.6,1],'color','r')
line([size(Result_base.times,1)*fanoParams.boxWidth,size(Result_base.times,1)*fanoParams.boxWidth],...
[0.6,1],'color','r')
line(onsetT(1:clipend), norm_base_CI(1:clipend,1),'color',[0.5 0.5 0.5])
line(onsetT(1:clipend), norm_base_CI(1:clipend,2),'color',[0.5 0.5 0.5])
line(offsetT(clipon:end),norm_base_CI_end(clipon:end,1),'color',[0.5 0.5 0.5])
line(offsetT(clipon:end),norm_base_CI_end(clipon:end,2),'color',[0.5 0.5 0.5])
medianFano = median(norm_base(onsetind:clipend))
CI = getCDFconf(norm_base(onsetind:clipend),95)
medianCIacrossTime = median(norm_base_CI(onsetind:clipend,:))
numconditions = size(Result_pre.meanRateAll_Trials,1)
[h,p]=kstest([norm_base(onsetind:clipend)',norm_base(1:onsetind)'])
[h,p]=kstest([Result_base.FanoFactor(onsetind:clipend)',Result_base.FanoFactor(1:onsetind)'])
% make figure for onset align and offset align of mean and FF using % baseline not absolute
%plotted on same axes for making figure
hfig = figure;
hold on
onsetT = Result_base.times;
clipend = find(Result_base.times == 2000);
offsetT = Result_base_end.times + size(Result_base.times,1)*fanoParams.boxWidth;
clipon = find(Result_base_end.times == -2000);
line(onsetT(1:clipend),norm_base(1:clipend),'color','k')
line(offsetT(clipon:end),norm_base_end(clipon:end),'color','k')
line(onsetT(1:clipend),norm_gaba(1:clipend),'color','r')
line(offsetT(clipon:end),norm_gaba_end(clipon:end),'color','r')
line([0,0],[0.6,1],'color','r')
line([size(Result_base.times,1)*fanoParams.boxWidth,size(Result_base.times,1)*fanoParams.boxWidth],...
[0.6,1],'color','r')
% saveas(hfig,'/Volumes/kperks/Documents/EJN/Figures/EPSforFIG4/NormFF.fig')
%mean rates across both conditions plotted on same axes for making figure
hfig = figure;
hold on
onsetT = Result_base.times;
clipend = find(Result_base.times == 2000);
offsetT = Result_base_end.times + size(Result_base.times,1)*fanoParams.boxWidth;
clipon = find(Result_base_end.times == -2000);
line(onsetT(1:clipend),Result_base.meanRateAll(1:clipend))
line(offsetT(clipon:end),Result_base_end.meanRateAll(clipon:end))
line(onsetT(1:clipend),Result_gz.meanRateAll(1:clipend),'color','r')
line(offsetT(clipon:end),Result_gz_end.meanRateAll(clipon:end),'color','r')
line([0,0],[0,12],'color','r')
line([size(Result_base.times,1)*fanoParams.boxWidth,size(Result_base.times,1)*fanoParams.boxWidth],...
[0,12],'color','r')
prestimRate = mean(Result_base.meanRateAll(1:onsetind))
% saveas(hfig,'/Volumes/kperks/Documents/EJN/Figures/EPSforFIG4/NormRates.fig')
%normalized to max for both conditions at stim onset and offset
%for figure on same time course for intact and gabazine
hfig = figure;
hold on
onsetT = Result_base.times;
clipend = find(Result_base.times == 2000);
offsetT = Result_base_end.times + size(Result_base.times,1)*fanoParams.boxWidth;
clipon = find(Result_base_end.times == -2000);
line(onsetT(1:clipend),Result_base.FanoFactor(1:clipend)/max(Result_base.FanoFactor(1:clipend)),'color','k')
line(offsetT(clipon:end),Result_base_end.FanoFactor(clipon:end)/max(Result_base_end.FanoFactor(clipon:end)),'color','k')
line(onsetT(1:clipend),Result_gz.FanoFactor(1:clipend)/max(Result_gz.FanoFactor(1:clipend)),'color','r')
line(offsetT(clipon:end),Result_gz_end.FanoFactor(clipon:end)/max(Result_gz_end.FanoFactor(clipon:end)),'color','r')
line([0,0],[0.6,1],'color','r')
line([size(Result_base.times,1)*fanoParams.boxWidth,size(Result_base.times,1)*fanoParams.boxWidth],...
[0.6,1],'color','r')
%scatter of mean rates to get a a sense of scale and offset
figure;hold on
scatter(Result_base.meanRateAll,Result_gz.meanRateAll)
scatter(Result_base_end.meanRateAll,Result_gz_end.meanRateAll)
line([0,25],[0,25],'color','r')
axis tight
axis image
%%%%%%%%%%%%
% get fits for onset and offset under both conditions
%onset
options = fitoptions('exp1');
lowerTau = -1/20;
upperTau = -1/700;
options.Lower = [0,lowerTau];
options.Upper = [Inf,upperTau];
fitT = Result_base.times(onsetind:end);
fitY = norm_base(onsetind:end) - meanDropFF_base;
figure;hold on
line(fitT,fitY)
cf = fit(fitT,fitY,'exp1',options);
fitline = cf.a*exp(cf.b*fitT);
line(fitT,fitline,'color','r')
onsetTau = -1/cf.b
figure;hold on
line(Result_base.times,norm_base,'color','k')
line(fitT,fitline + meanDropFF_base,'color','r')
% set(gca,'XLim',[-500,500],'YLim',[0.6,1.2])
%offset
options = fitoptions('exp1');
lowerTau = 1/20;
upperTau = 1/700;
options.Lower = [0,-Inf];
options.Upper = [Inf,Inf];
stopfit = find(Result_base_end.times == 500)
fitT = Result_base_end.times(1:stopfit);
fitY = norm_base_end(1:stopfit) - meanDropFFend_base;
figure;hold on
line(fitT,fitY)
cf = fit(fitT,fitY,'exp1',options);
fitline = cf.a*exp(cf.b*fitT);
line(fitT,fitline,'color','r')
offsetTau = -1/cf.b
figure;hold on
line(Result_base_end.times,norm_base_end,'color','k')
line(fitT,fitline + meanDropFFend_base,'color','r')
% set(gca,'XLim',[-500,1000],'YLim',[0.5,1.5])
% make figure for onset align and offset align of mean and FF using % baseline not absolute
hfig = figure;
hold on
onsetT = Result_base.times;
clipend = find(Result_base.times == 2000);
line(onsetT(1:clipend),norm_base(1:clipend),'color','k')
line(onsetT(1:clipend),norm_gaba(1:clipend),'color','r')
%onset
options = fitoptions('exp1');
lowerTau = -1/20;
upperTau = -1/700;
options.Lower = [0,lowerTau];
options.Upper = [Inf,upperTau];
fitT = Result_base.times(onsetind:end);
fitY = norm_base(onsetind:end) - meanDropFF_base;
cf = fit(fitT,fitY,'exp1',options);
fitline = cf.a*exp(cf.b*fitT);
onsetTau = -1/cf.b
line(fitT,fitline + meanDropFF_base,'color','g')
offsetT = Result_base_end.times + size(Result_base.times,1)*fanoParams.boxWidth;
clipon = find(Result_base_end.times == -2000);
line(offsetT(clipon:end),norm_base_end(clipon:end),'color','k')
line(offsetT(clipon:end),norm_gaba_end(clipon:end),'color','r')
%offset
options = fitoptions('exp1');
options.Lower = [0,-Inf];
options.Upper = [Inf,Inf];
stopfit = find(Result_base_end.times == 500)
fitT = Result_base_end.times(1:stopfit);
fitY = norm_base_end(1:stopfit) - meanDropFFend_base;
cf = fit(fitT,fitY,'exp1',options);
fitline = cf.a*exp(cf.b*fitT);
offsetTau = -1/cf.b
line(fitT+size(Result_base.times,1)*fanoParams.boxWidth,fitline + meanDropFFend_base,'color','g')
line([0,0],[0.6,1],'color','b')
line([size(Result_base.times,1)*fanoParams.boxWidth,size(Result_base.times,1)*fanoParams.boxWidth],...
[0.6,1],'color','b')
axis tight
saveas(hfig,'/Volumes/kperks/Documents/EJN/Figures/EPSforFIG4/NormFF_on_off_withFIT.fig')
saveas(hfig,'/Volumes/kperks/Documents/EJN/Figures/EPSforFIG4/NormFF_on_off_withFIT.jpg')
%onset gaba
options = fitoptions('exp1');
lowerTau = -1/20;
upperTau = -1/700;
options.Lower = [0,lowerTau];
options.Upper = [Inf,upperTau];
fitT = Result_gz.times(onsetind:end);
fitY = norm_gaba(onsetind:end) - meanDropFF_gaba;
figure;hold on
line(fitT,fitY,'color','r')
cf = fit(fitT,fitY,'exp1',options);
fitline_on_gaba = cf.a*exp(cf.b*fitT);
line(fitT,fitline_on_gaba,'color','g')
onsetTau_gaba = -1/cf.b
%offset gaba
options = fitoptions('exp1');
options.Lower = [0,-Inf];
options.Upper = [Inf,Inf];
stopfit = find(Result_gz_end.times == 500)
fitT_end_gaba = Result_gz_end.times(1:stopfit);
fitY = norm_gaba_end(1:stopfit) - meanDropFFend_gaba;
figure;hold on
line(fitT_end_gaba,fitY,'color','r')
cf = fit(fitT_end_gaba,fitY,'exp1',options);
fitline_off_gaba = cf.a*exp(cf.b*fitT_end_gaba);
line(fitT_end_gaba,fitline_off_gaba,'color','g')
offsetTau_gaba = -1/cf.b
%
%
% hfig = figure;
% hold on
% onsetT = Result_base_end.times;
% clipon = find(Result_base_end.times == -2000);
% line(onsetT(clipon:end),norm_base_end(clipon:end),'color','k')
% line(onsetT(clipon:end),norm_gaba_end(clipon:end),'color','r')
% %onset
% options = fitoptions('exp1');
% lowerTau = -1/20;
% upperTau = -1/700;
% options.Lower = [0,lowerTau];
% options.Upper = [Inf,upperTau];
% fitT = Result_gz.times(onsetind:end);
% fitY = norm_gaba(onsetind:end) - meanDropFF_gaba;
% cf = fit(fitT,fitY,'exp1',options);
% fitline_on_gaba = cf.a*exp(cf.b*fitT);
% onsetTau_gaba = -1/cf.b
% line(fitT,fitline_on_gaba + meanDropFF_gaba,'color','g')
%
% offsetT = Result_base_end.times + size(Result_base.times,1)*fanoParams.boxWidth;
% clipon = find(Result_base_end.times == -2000);
% line(offsetT(clipon:end),norm_base_end(clipon:end),'color','k')
% line(offsetT(clipon:end),norm_gaba_end(clipon:end),'color','r')
% %offset
% options = fitoptions('exp1');
% options.Lower = [0,-Inf];
% options.Upper = [Inf,Inf];
% stopfit = find(Result_base_end.times == 700)
% fitT = Result_base_end.times(1:stopfit);
% fitY = norm_base_end(1:stopfit) - meanDropFFend_base;
% cf = fit(fitT,fitY,'exp1',options);
% fitline = cf.a*exp(cf.b*fitT);
% offsetTau = -1/cf.b
% line(fitT+size(Result_base.times,1)*fanoParams.boxWidth,fitline + meanDropFFend_base,'color','g')
%
% line([0,0],[0.6,1],'color','b')
% line([size(Result_base.times,1)*fanoParams.boxWidth,size(Result_base.times,1)*fanoParams.boxWidth],...
% [0.6,1],'color','b')
% axis tight
%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%
%% Do the FanoFactor analysis across all cells...
times = 25:50:6000; % from 1950 ms before target onset until 2000 ms after.
fanoParams.alignTime = 1975; % this time will become zero time fanoParams.boxWidth = 50; % 50 ms sliding window.
fanoParams.matchReps = 10;
fanoParams.binSpacing = 0.25;
fanoParams.boxWidth = 50;
Result_base = VarVsMean(base_data_All, times, fanoParams);
plotFano(Result_base);
figure;hold on
line(Result_base.times,Result_base.FanoFactor','color','r')
line(Result_base.times,Result_base.FanoFactorAll','color','k')
legend('meanMatched','unmatched')
ylabel('FanoFactor', 'FontSize',14);
xlabel('milliseconds','FontSize',14);
% mv = ScatterMovie(Result_base);
% yourName = '/Users/kperks/GitHub/iontoncm/FANOanalysis/baseline_condition_matched.avi';
% movie2avi(mv, yourName, 'FPS', 15, 'compression', 'none');
Result_gz = VarVsMean(gz_data_All, times, fanoParams);
plotFano(Result_gz);
figure;hold on
line(Result_gz.times,Result_gz.FanoFactor','color','r')
line(Result_gz.times,Result_gz.FanoFactorAll','color','k')
legend('meanMatched','unmatched')
ylabel('FanoFactor', 'FontSize',14);
xlabel('milliseconds','FontSize',14);
% mv = ScatterMovie(Result_base);
% yourName = '/Users/kperks/GitHub/iontoncm/FANOanalysis/InhibitionBlocked_condition_matched.avi';
% movie2avi(mv, yourName, 'FPS', 15, 'compression', 'none');
figure;hold on
line(Result_base.times,Result_base.meanRateAll,'color','k')
line(Result_gz.times,Result_gz.meanRateAll,'color','r')
axis tight
%
% figure;hold on
% plot(Result_base.FanoFactorAll,'color','k')
% plot(Result_gz.FanoFactorAll,'color','r')
% axis tight
%
% %when did mean matching...
% figure;hold on
% plot(Result_base.meanRateSelect,'color','k')
% plot(Result_gz.meanRateSelect,'color','r')
% axis tight
figure;hold on
plot(Result_base.times,Result_base.FanoFactor,'color','k')
plot(Result_base.times,Result_gz.FanoFactor,'color','r')
axis tight
% plot as a % of mean baseline FF and quantify
onsetind = max(find(Result_base.times <= 0))
prestimFF_base = mean(Result_base.FanoFactor(1:onsetind));
prestimFF_gz = mean(Result_gz.FanoFactor(1:onsetind));
norm_base = Result_base.FanoFactor / mean(Result_base.FanoFactor(1:onsetind));
meanDropFF_base = mean(norm_base(onsetind+5:end));
norm_gaba = Result_gz.FanoFactor / mean(Result_gz.FanoFactor(1:onsetind));
meanDropFF_gaba = mean(norm_gaba(onsetind+5:end));
figure;hold on
plot(Result_base.times , norm_base,'color','k')
plot(Result_base.times , norm_gaba,'color','r')
norm_base_onsetAlign = norm_base;
% plot aligned to offset results as % pre-stim mean
offsetind = max(find(Result_base_end.times < 0))
norm_base_end = Result_base_end.FanoFactor / prestimFF_base;
meanDropFFend_base = mean(norm_base_end(5:offsetind-5));
norm_gaba_end = Result_gz_end.FanoFactor / prestimFF_gz;
meanDropFFend_gaba = mean(norm_gaba_end(5:offsetind-5));
figure;hold on
plot(Result_base_end.times , norm_base_end,'color','k')
plot(Result_base_end.times , norm_gaba_end,'color','r')
avgdrop_base = mean([meanDropFF_base,meanDropFFend_base])
avgdrop_gz = mean([meanDropFF_gaba,meanDropFFend_gaba])
%% re-make figure for onset align and offset align of mean and FF using % baseline not absolute
hfig = figure;
hold on
onsetT = Result_base.times;
clipend = find(Result_base.times == 2000)
offsetT = Result_base_end.times + size(Result_base.times,1)*fanoParams.boxWidth;
clipon = find(Result_base_end.times == -2000)
line(onsetT(1:clipend),norm_base(1:clipend),'color','k')
line(offsetT(clipon:end),norm_base_end(clipon:end),'color','k')
line(onsetT(1:clipend),norm_gaba(1:clipend),'color','r')
line(offsetT(clipon:end),norm_gaba_end(clipon:end),'color','r')
line([0,0],[0.6,1],'color','r')
line([size(Result_base.times,1)*fanoParams.boxWidth,size(Result_base.times,1)*fanoParams.boxWidth],...
[0.6,1],'color','r')
saveas(hfig,'/Volumes/kperks/Documents/EJN/Figures/EPSforFIG4/NormFF.fig')
figure;
hold on
onsetT = Result_base.times;
clipend = find(Result_base.times == 2000)
offsetT = Result_base_end.times + size(Result_base.times,1)*fanoParams.boxWidth;
clipon = find(Result_base_end.times == -2000)
line(onsetT(1:clipend),Result_base.meanRateAll(1:clipend))
line(offsetT(clipon:end),Result_base_end.meanRateAll(clipon:end))
line(onsetT(1:clipend),Result_gz.meanRateAll(1:clipend),'color','r')
line(offsetT(clipon:end),Result_gz_end.meanRateAll(clipon:end),'color','r')
line([0,0],[0,12],'color','r')
line([size(Result_base.times,1)*fanoParams.boxWidth,size(Result_base.times,1)*fanoParams.boxWidth],...
[0,12],'color','r')
saveas(hfig,'/Volumes/kperks/Documents/EJN/Figures/EPSforFIG4/NormRates.fig')
figure;hold on
scatter(Result_base.meanRateAll,Result_gz.meanRateAll)
scatter(Result_base_end.meanRateAll,Result_gz_end.meanRateAll)
line([0,25],[0,25],'color','r')
axis tight
axis image
prestimRate = mean(Result_base.meanRateAll(1:onsetind))
%% fit normalized (by baseline mean) FF curves to get tau
%onset