File contents

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Generates figures for previously computed patterns
% April 2016
% Author: L. Muresan, lam94@cam.ac.uk
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Parameters to be modified by the user

CorP = 1; % if 1 all the plots are CenterToPeriphery,otherwise - PeripheryToCenter
saveim = 1; % if 1 all images are automatically saved
sep = '/'; % for Mac /
%%
if CorP ~= 1
    CorP =2;
end
option{1} = 'CtoP'; %CenterToPeriphery
option{2} = 'PtoC'; %PeripheryToCenter

% Read computed patterns
pt = uigetdir();
fls = dir(strcat(pt,'/*',option{CorP},'.csv'));
if exist('R')
    clear R
end
if length(fls) == 0
    msgbox('No result csv files found! Run ComputePatterns first.')

else

    for k = 1:length(fls)
        R{k}= csvread(strcat(pt,sep, fls(k).name));
    end
    %% all profiles
    clear tG tR tC

    h = figure;
    x = 0:0.01:1;
    for k = 1:length(R)    
        vG{k} = interp1(R{k}(:,1)/max(R{k}(:,1)),  R{k}(:,2)/sum(R{k}(:,2)), x); 
        if CorP ==1
            tG(k,:) = vG{k};
        else
            tG(k,:) = fliplr(vG{k})/sum(vG{k});
        end
        plot(x,  tG(k,:), 'g'); hold on
    end

    for k = 1:length(R)    
        vR{k} = interp1(R{k}(:,1)/max(R{k}(:,1)),  R{k}(:,3)/sum(R{k}(:,3)), x);
        if CorP ==1
            tR(k,:) = vR{k};
        else
            tR(k,:) = fliplr(vR{k})/sum(vR{k});
        end
        plot(x,  tR(k,:), 'r'); hold on
    end

    for k = 1:length(R)    
        vC{k} = interp1(R{k}(:,1)/max(R{k}(:,1)),  R{k}(:,4)/sum(R{k}(:,4)), x);
        if CorP ==1
            tC(k,:) = vC{k};
        else
            tC(k,:) = fliplr(vC{k})/sum(vC{k});
        end
        plot(x,  tC(k,:), 'c'); hold on
    end

    title (['All samples profiles. ', ' ', option{CorP}]), 
    if CorP ==1
        xlabel('Normalised distance from centre to periphery');
    else
        xlabel('Normalised distance from  periphery to centre');
    end
    ylabel('Normalised fluorescence intensity'); 
    if saveim
        print(h, strcat(pt,sep,'Fig','All samples_profiles_', option{CorP},'.pdf'),'-dpdf');
        savefig(h, strcat(pt,sep,'Fig','All samples_profiles_', option{CorP},'.fig'));
    end

    %% Single profile figures. Uncomment below if you want each profile figure saved separately.

    % for k = 1:size(tR,1)
    %     h = figure;
    %     plot(x,  tR(k,:), 'r', 'LineWidth',2); hold on
    %     plot(x,  tG(k,:), 'g', 'LineWidth',2); 
    %     plot(x,  tC(k,:), 'c', 'LineWidth',2); 
    %     
    %     if CorP ==1
    %         xlabel('Normalised distance from centre to periphery');
    %     else
    %         xlabel('Normalised distance from  periphery to centre');
    %     end
    %     ylabel('Normalised fluorescence intensity'); 
    %     title(strcat(strtok(fls(k).name, '.') ));    
    %     if saveim
    %         print(h, strcat(pt,sep,'Fig',strtok(fls(k).name, '.'), '.pdf'),'-dpdf');
    %         savefig(h,  strcat(pt,sep,'Fig',strtok(fls(k).name, '.'), '.fig'));
    %     end
    % end  
    %%
    mG = mean(tG);
    sG = std(tG);

    mR = mean(tR);
    sR = std(tR);

    mC = mean(tC);
    sC = std(tC);


    %% ecdf single profiles.  Uncomment below if you want each ecdf figure saved separately.

    % for k = 1:size(tR,1)
    %     h = figure;
    %     plot(cumsum(tR(k,:)), 'r', 'LineWidth',2); hold on
    %     plot(cumsum(tG(k,:)),'g', 'LineWidth',2)
    %     plot(cumsum(tC(k,:)),'c', 'LineWidth',2)
    %     line([0 length(tR(k,:))], [1 1 ], 'Color', 'k', 'LineStyle',':')
    %     ylim([0 1.05])
    %     xlabel('Radius (ru)')
    %     ylabel('ecdf')
    %     title(strcat(strtok(fls(k).name, '.'), option{CorP} ,' ecdf'));    
    %     if saveim
    %         print(h, strcat(pt,sep,'Fig',strtok(fls(k).name, '.'), '_ecdf.pdf'),'-dpdf');
    %         savefig(h,  strcat(pt,sep,'Fig',strtok(fls(k).name, '.'), '_ecdf.fig'));
    %     end
    % end

    %% ecdf  all profiles

    if size(tR,1)>1
        h = figure;
        shadedErrorBar(x, mG, sG, 'g', 0.8); hold on
        shadedErrorBar(x, mR, sR, 'r', 0.8); 
        shadedErrorBar(x, mC, sC, 'c', 0.8); 
        plot(x,mG, 'g', 'LineWidth',3); hold on
        plot(x,mR, 'r', 'LineWidth',3)
        plot(x,mC, 'c', 'LineWidth', 3)    

        axis tight
        title (['All samples profiles ', option{CorP}, ' with error']); 
        if CorP ==1
            xlabel('Normalised distance from centre to periphery');
        else
            xlabel('Normalised distance from  periphery to centre');
        end
        ylabel('Normalised fluorescence intensity');

        if saveim
            print(h, strcat(pt,sep,'Fig','All samples_profiles_', option{CorP},'_with_error.pdf'),'-dpdf');
            savefig(h,  strcat(pt,sep,'Fig','All samples_profiles_', option{CorP},'_with_error.fig'));
        end    
    end

    %% area measurements

    for k = 1:size(tR,1)
        areaR = trapz(cumsum(tR(k,:)));
        areaC = trapz(cumsum(tC(k,:)));
        areaG = trapz(cumsum(tG(k,:)));
        areaDiff = areaC - areaG;
        area(k,1) = areaR;
        area(k,2) = areaC;
        area(k,3) = areaG;
        area(k,4) = areaDiff;
    end

    hdr={'AUC RFP (au)','AUC CFP (au)','AUC GFP (au)','AUC CFP - AUC GFP (au)'};
    txt=sprintf('%s,',hdr{:});
    txt(end)='';
    dlmwrite(strcat(pt,sep,'Area_measurements.csv'),txt, '');
    dlmwrite(strcat(pt,sep,'Area_measurements.csv'),area, '-append'); 
    save(strcat(pt,sep,'Area_measurements.mat'),'area');

    %% all ecdf

    for k = 1:size(tR,1)
        cumR(k,:) = cumsum(tR(k,:)); cumR(k,:) = cumR(k,:)./cumR(k,101);
        cumG(k,:) = cumsum(tG(k,:)); cumG(k,:) = cumG(k,:)./cumG(k,101);
        cumC(k,:) = cumsum(tC(k,:)); cumC(k,:) = cumC(k,:)./cumC(k,101);
    end

    mG = mean(cumG);
    sG = std(cumG);
    mR = mean(cumR);
    sR = std(cumR);
    mC = mean(cumC);
    sC = std(cumC);

    if size(tR,1)>1
        h = figure;
        shadedErrorBar(x, mG, sG, 'g', 0.8); hold on % 'Marker', '*','MarkerSize',6
        shadedErrorBar(x, mC, sC, 'c', 0.8);
        plot(x,mG, 'g', 'LineWidth',3); hold on
        plot(x,mC, 'c', 'LineWidth',3)    
        % commentout next two lines if you want ecdf for RFP
        % plot(x,mR, 'r', 'LineWidth',3) 
        % shadedErrorBar(x, mR, sR, 'r', 0.8);
        xlabel('Radius (ru)')
        ylabel('ecdf')
        axis tight
        line([0 1], [0 1], 'LineStyle', ':', 'Color','k')
        title (['All samples ecdfs ', ' ', option{CorP}, ' with error']);

        if saveim    
            print(h, strcat(pt,sep,'Fig','All samples_ecdf_', option{CorP} ,'ecdf.pdf'),'-dpdf');
            savefig(h, strcat(pt,sep,'Fig','All samples_ecdf_', option{CorP} ,'ecdf.fig'))
        end    
    end

end