dLGN_plot_analysis.m

function [ramps_peak ODI data]=dLGN_plot_analysis(directory,plotyn)
%SW181229
%Function for claculating and plotting extracted dLGN ephys data. This
%function uses the extracted ephys data gnerated with script Analysis_mini_ramp as an input

%Inputs:
%directory: directory of extracted mat file gnerated with script Analysis_mini_ramp

%NESTED FUNCTION:
%barwitherr
%uipickfiles

filename=uipickfiles('FilterSpec',directory)%pathname, you need uipickfiles function
load(char(filename));%load mat file
%% RAMP ANALYSIS
%%LOAD PEAK AMPLITUDES FOR AMPA and NMDA
for i=1:(size(data,1)-1)
    %AMPA
    blue_ramp_70(:,i)=data{i+1,4}.neg_peak2(1,:);
    blue_laser_70(:,i)=data{i+1,4}.laser_amp(1,:);
    red_ramp_70(:,i)=data{i+1,5}.neg_peak1(2,:);
    red_laser_70(:,i)=data{i+1,5}.laser_amp(2,:);
    blue_constant_70(:,i)=data{i+1,4}.neg_peak2(2,:);
    blue_claser_70(:,i)=data{i+1,4}.laser_amp(2,:);
    %NMDA
    blue_ramp_40(:,i)=data{i+1,4}.pos_peak2(3,:);
    blue_laser_40(:,i)=data{i+1,4}.laser_amp(3,:);
    red_ramp_40(:,i)=data{i+1,5}.pos_peak1(4,:);
    red_laser_40(:,i)=data{i+1,5}.laser_amp(4,:);
    blue_constant_40(:,i)=data{i+1,4}.pos_peak2(4,:);
    blue_claser_40(:,i)=data{i+1,4}.laser_amp(4,:);
end
i=[];
%%
%SET VALUES BELOW STD THRESHOLD CRITERION TO ZERO
for i=1:(length(data)-1)
    %%%%%%%BLUE ONLY AMPA
    idx=find(data{i+1,4}.neg_fail2(1,:)>0)';
    d=data{i+1,4}.neg_peak2(1,:);
    %%%%%%%
    ze=zeros(11,1);
    if length(idx)>=5;
        ze(idx)=d(idx);
        b_r_70(:,i)=ze ;
    else
        b_r_70(:,i)=ze;
    end
    %%%%%%%
    idx=[];
    d=[];
    ze=[];
    %%%%%%%RED AMPA
    idx=find(data{i+1,5}.neg_fail1(2,:)>0)';
    d=data{i+1,5}.neg_peak1(2,:);
    %%%%%%%
    ze=zeros(11,1);
    if length(idx)>=5;
        ze(idx)=d(idx);
        r_r_70(:,i)=ze;
    else
        r_r_70(:,i)=ze;
    end
    %%%%%%%
    idx=[];
    d=[];
    ze=[];
    %%%%%%%BLUE CONSTANT AMPA
    idx=find(data{i+1,4}.neg_fail2(2,:)>0)';
    d=data{i+1,4}.neg_peak2(2,:);
    %%%%%%%
    ze=zeros(11,1);
    if length(idx)>=5;
        ze(idx)=d(idx);
        b_c_70(:,i)=ze;
    else
        b_c_70(:,i)=ze;
    end
    %%%%%%%
    idx=[];
    d=[];
    ze=[];
    %%%%%%%BLUE ONLY NMDA
    idx=find(data{i+1,4}.pos_fail2(3,:)>0)';
    d=data{i+1,4}.pos_peak2(3,:);
    %%%%%%%
    ze=zeros(11,1);
    if length(idx)>=5;
        ze(idx)=d(idx);
        b_r_40(:,i)=ze ;
    else
        b_r_40(:,i)=ze;
    end
    %%%%%%%
    idx=[];
    d=[];
    ze=[];
    %%%%%%%RED NMDA
    idx=find(data{i+1,5}.pos_fail1(4,:)>0)';
    d=data{i+1,5}.pos_peak1(4,:);
    %%%%%%%
    ze=zeros(11,1);
    if length(idx)>=5;
        ze(idx)=d(idx);
        r_r_40(:,i)=ze;
    else
        r_r_40(:,i)=ze;
    end
    %%%%%%%
    idx=[];
    d=[];
    ze=[];
    %%%%%%%BLUE CONSTANT NMDA
    idx=find(data{i+1,4}.pos_fail2(4,:)>0)';
    d=data{i+1,4}.pos_peak2(4,:);
    %%%%%%%
    ze=zeros(11,1);
    if length(idx)>=5;
        ze(idx)=d(idx);
        b_c_40(:,i)=ze;
    else
        b_c_40(:,i)=ze;
    end
    %%%%%%%
    idx=[];
    d=[];
    ze=[];
end
%%
%ODI and AMPA/NMDA Ratio
for i=1:(length(data)-1)
    %AMPA
    ODI_raw_AMPA(:,i)=(abs(red_ramp_70(:,i))-abs(blue_constant_70(:,i)))./(abs(red_ramp_70(:,i))+abs(blue_constant_70(:,i)));
    ODI_AMPA(:,i)=(abs(r_r_70(:,i))-abs(b_c_70(:,i)))./(abs(r_r_70(:,i))+abs(b_c_70(:,i)));
    %NMDA
    ODI_raw_NMDA(:,i)=(abs(red_ramp_40(:,i))-abs(blue_constant_40(:,i)))./(abs(red_ramp_40(:,i))+abs(blue_constant_40(:,i)));
    ODI_NMDA(:,i)=(abs(r_r_40(:,i))-abs(b_c_40(:,i)))./(abs(r_r_40(:,i))+abs(b_c_40(:,i)));
    %AMPA/NMDA Ratio
    Ratio_an_r(:,i)=abs(r_r_70(:,i))./abs(r_r_40(:,i));
    Ratio_an_b(:,i)=abs(b_r_70(:,i))./abs(b_r_40(:,i));
    Ratio_an_bc(:,i)=abs(b_c_70(:,i))./abs(b_c_40(:,i));
end
%ODI average; used the last 6 entries from 11 ramps-> NEEDS TO BE DISCUSSED
ODI_A=nanmean(ODI_AMPA(5:end,:));
ODI_A_sem=nanstd(ODI_AMPA(5:end,:))/sqrt(length(data));
ODI_N=nanmean(ODI_NMDA(5:end,:));
ODI_N_sem=nanstd(ODI_NMDA(5:end,:))/sqrt(length(data));
%RATIO AMPA/NMDA average
R_r=nanmean(Ratio_an_r(5:end,:));
R_r_sem=nanstd(Ratio_an_r(5:end,:))/sqrt(length(data));
R_b=nanmean(Ratio_an_b(5:end,:));
R_b_sem=nanstd(Ratio_an_b(5:end,:))/sqrt(length(data));
R_bc=nanmean(Ratio_an_bc(5:end,:));
R_bc_sem=nanstd(Ratio_an_bc(5:end,:))/sqrt(length(data));
%Create combined vector for plotting in bar graph later
com_ODI=[ODI_A' ODI_N'];
com_ODI_sem=[ODI_A_sem' ODI_N_sem'];
com_R=[R_b' R_r' R_bc'];
com_R_sem=[R_b_sem' R_r_sem' R_bc_sem'];

%output important variables

ramps_peak.red70=r_r_70;
ramps_peak.red40=r_r_40;
ramps_peak.blue70=b_r_70;
ramps_peak.blue40=b_r_40;
ramps_peak.blue_constant70=b_c_70;
ramps_peak.blue_constant40=b_c_40;
ODI.AMPA=ODI_AMPA;
ODI.NMDA=ODI_NMDA;
ODI.aAMPA=ODI_A;
ODI.aNMDA=ODI_N;

data{1,7}='ODI AMPA';
data{1,8}='ODI NMDA';

for i=1:(length(data)-1)
    data{i+1,7}=ODI_A(i);
    data{i+1,8}=ODI_N(i);
end

%%
i=[];
if plotyn==1
    %PLOT GRAPHS
    cvec=unique(hsv(length(data)*30),'rows');
    Legend=cell(length(data),1)%  two positions
    f1=figure('Name','AMPA');
    set(gcf, 'Position', [200, 0, 600, 1500]);
    f2=figure('Name','NMDA');
    set(gcf, 'Position', [600, 0, 600, 1500]);
    
    for i=1:(length(data)-1)
        figure(f1);
        subplot(3,1,1);
        h{i}=plot(blue_laser_70(:,i),b_r_70(:,i),'--s','LineWidth',2,'MarkerSize',5,'Color',cvec(i*30,:));
        axis square;
        title('Blue laser only');
        xlabel('Laser amplitude (a.u.)');
        ylabel('Peak synaptic current (pA)');
        Legend{i}=data{i,1};
        hold on;
    end
    figure(f1);
    legend(Legend,'Location','EastOutside');
    legend boxoff;
    hold on;
    i=[];
    %%%second repeat
    for i=1:(length(data)-1)
        subplot(3,1,2);
        m{i}=plot(blue_laser_70(:,i),r_r_70(:,i),'--s','LineWidth',2,'MarkerSize',5,'Color',cvec(i*30,:));
        title('Red laser');
        xlabel('Laser amplitude (a.u.)');
        ylabel('Peak synaptic current (pA)');
        axis square;
        hold on;
    end
    figure(f1);
    legend(Legend,'Location','EastOutside');
    legend boxoff;
    hold on;
    i=[];
    %%%third repeat
    for i=1:(length(data)-1)
        subplot(3,1,3);
        m{i}=plot(blue_claser_70(:,i),b_c_70(:,i),'--s','LineWidth',2,'MarkerSize',5,'Color',cvec(i*30,:));
        title('Blue constant');
        xlabel('Laser amplitude (a.u.)');
        ylabel('Peak synaptic current (pA)');
        axis square;
        hold on;
    end
    figure(f1);
    legend(Legend,'Location','EastOutside');
    legend boxoff;
    hold on;
    i=[];
    
    %40mV NMDA
    %1st repeat
    figure(f2);
    for i=1:(length(data)-1)
        subplot(3,1,1);
        m{i}=plot(blue_laser_40(:,i),b_r_40(:,i),'--s','LineWidth',2,'MarkerSize',5,'Color',cvec(i*30,:));
        title('Blue laser only');
        xlabel('Laser amplitude (a.u.)');
        ylabel('Peak synaptic current (pA)');
        axis square;
        Legend{i}=data{i,1};
        hold on;
    end
    figure(f2);
    legend(Legend,'Location','EastOutside');
    legend boxoff;
    hold on;
    i=[];
    %2nd repeat
    for i=1:(length(data)-1)
        subplot(3,1,2);
        m{i}=plot(blue_laser_40(:,i),r_r_40(:,i),'--s','LineWidth',2,'MarkerSize',5,'Color',cvec(i*30,:));
        title('Red laser');
        xlabel('Laser amplitude (a.u.)');
        ylabel('Peak synaptic current (pA)');
        axis square;
        Legend{i}=data{i,1};
        hold on;
    end
    figure(f2);
    legend(Legend,'Location','EastOutside');
    legend boxoff;
    hold on;
    i=[];
    %3rd repeat
    for i=1:(length(data)-1)
        subplot(3,1,3);
        m{i}=plot(blue_claser_40(:,i),b_c_40(:,i),'--s','LineWidth',2,'MarkerSize',5,'Color',cvec(i*30,:));
        title('Blue constant');
        xlabel('Laser amplitude (a.u.)');
        ylabel('Peak synaptic current (pA)');
        axis square;
        Legend{i}=data{i,1};
        hold on;
    end
    figure(f2);
    legend(Legend,'Location','EastOutside');
    legend boxoff;
    hold on;
    i=[];
    
    %ODI AND RATIO AMPA/NMDA
    %ODI
    try
        figure;barwitherr(com_ODI_sem,com_ODI);
    catch
        figure;bar(com_ODI);hold on;errorbar(com_ODI,com_ODI_sem,'.');
    end
    ylim([-1.3 1.3])
    axis square;
    xlabel('Cell');
    ylabel('ODI');
    title('Ocular dominance');
    legend('AMPA','NMDA');
    %RATIO AMPA/NMDA
    try
        figure;barwitherr(com_R_sem,com_R);
    catch
        figure;bar(com_R);hold on;errorbar(com_R,com_R_sem,'.');
    end
    axis square;
    xlabel('Cell');
    ylabel('Peak AMPA / Peak NMDA');
    title('AMPA / NMDA Ratio');
    legend('Blue only','Red','Blue constant');
    %% MINI ANALYSIS
    % %AMPA
    % i_o_suc=zeros(1,size(data,1));
    % i_o_suc_sem=zeros(1,size(data,1));
    % minionly=1;
    % for i=1:size(data,1)
    % if minionly==1;
    % try
    % mblue_70(:,i)=data{i,2}(1:50,1);
    % mred_70(:,i)=data{i,2}(1:50,2);
    % PD_blue_70(:,i)=data{i,4}(1:50,1);
    % PD_red_70(:,i)=data{i,4}(1:50,2);
    % IR1_red_70(:,i)=data{i,5}(1:50,2);
    % IR1_blue_70(:,i)=data{i,6}(1:50,2);
    % PD_rb_ratio(:,i)=mean(PD_red_70(:,i))/mean(IR1_blue_70(:,i));
    % IR_rb_ratio(:,i)=mean(IR1_red_70(:,i))/mean(IR1_blue_70(:,i));
    % catch
    % end
    % end
    % end
    %
    %
    % if length(find(mblue_70(:,i)<0))>5 & length(find(mred_70(:,i)<0))<7
    %     disp('IPSI ONLY');
    %     idx_success=find(mblue_70(1:50,i)<0);
    %     i_o_suc(:,i)=mean(mblue_70(idx_success));
    %     i_o_suc_sem(:,i)=std(mblue_70(idx_success,i))/length(sqrt(idx_success));
    % else
    %     disp ('EITHER CONTRA ONLY OR BINOCULAR');
    % end
    %
    % end
    %
    
    
    
    
end

end