single_cell_smooth.m

%% Plot two colors on the same figure
%% the age sort and death type selection are off
%%
clear all
load NAM_1000min_20160518; 
red = [1,0,0];
green = [0,1,0];

% all_data = input('Please type in the data set you want to plot,e.g. ''WT_20151112'': ');%Get the name of data
% Flu = input('Please type in the fluorescence channel you want to plot, e.g. [1 2] :');%Get the fluorescence channel number
% Label = input('Please type in the label for the fluorescence channel, e.g. ''NYN'' :');
% DT = input('Please type in what death type you want to plot, eg.. 1 : ');
% eval(['load ' all_data ';']);%load data
% eval(['all_data =' all_data ';']);%Rename the data want to plot to all_data
all_data = nestedSortStruct(NAM_1000min_20160518,'age');%Sort the data according to their lifespan
% all_data = all_data([all_data.Death_type] == DT);%Plot only death 1 and death 2


all_data = all_data([all_data.Death_type] == 1);
%Flu = input('Please type in the fluorescence channel you want to plot, e.g. [1 2] :');%Get the fluorescence channel number


for i=1:length(all_data)
    date = all_data(i).Date;
        date = num2str(date);
        if strcmp(date,'20160417')
            interval=6;
        else
            interval=15;
        end
    
%Get the max of axis
% max_x = zeros(1,length(all_data));%Create a empty array to store max of x axis of each cell
% max_y = zeros(2,length(all_data));%Create a empty array to store max of y axis of each cell


life_end = all_data(i).cycle(end);
        %Get the start frame of cell lifespan
        life_start = all_data(i).cycle(3);
        %Get the frames of lifespan for index fluorescence
        FLS = life_start:life_end;
        
        
        
curr_trace=all_data(i).traj_normalized((FLS),1,1);
xq=life_start:(1/interval):life_end;
curr_trace_i=interp1(FLS,curr_trace,xq,'Spline');

xq2=(life_start-1)*interval:(life_end-1)*interval;
FLS2 =(life_start-1)*interval:interval:(life_end-1)*interval;
r=600/length(curr_trace_i);
curr_trace_s = smooth(curr_trace_i,r,'rloess');

all_data_2(i).traj_i=curr_trace_i;
all_data_2(i).traj_s=curr_trace_s;
end
  
save('data_final_s2','all_data_2','all_data');


%     x_max=max(max(length(all_data_2.traj_i)));
%     y_max=max(max(all_data_2.traj_i));
% 
% % Specify how many each want for each subplot: Image Per Subplot
% IPS = input('please specifiy how many subplot per figure: pick 4,9,16,25 or 36 ');
% % Get the column and/or row number of each subplot: Column And Row
% CNR = sqrt(IPS);
% % Get the number of subplot is need: Number of Subplot
% NOS = ceil(length(all_data)/IPS);
% 
% 
% figure;
% for j=1:79
% figure;
% 
% figure;
% plot(FLS2,curr_trace,'k.','MarkerSize',10);
% hold on;
% plot(xq2,curr_trace_i,'b.','MarkerSize',5);
% hold on;
% plot(xq2,curr_trace_smooth,'r-','LineWidth',2);


% 
% end
% % for i_xy = 1:length(all_data)
%     max_x(i_xy) = all_data(i_xy).cycle(end)
%     %;%Get the last lifespan of the cell
%     max_y(1,i_xy) = max(all_data(i_xy).traj_normalized(all_data(i_xy).cycle(5):all_data(i_xy).cycle(end),:,Flu(1)));%Get the max flu during the current lifespan
%     max_y(2,i_xy) = max(all_data(i_xy).traj_normalized(all_data(i_xy).cycle(5):all_data(i_xy).cycle(end),:,Flu(2)));
% end
% max_y1 = max(max_y(1,:));
% max_y2 = max(max_y(2,:));
% max_x = max(max_x);
% 

% % Specify how many each want for each subplot: Image Per Subplot
% IPS = input('please specifiy how many subplot per figure: pick 4,9,16,25 or 36 ');
% % Get the column and/or row number of each subplot: Column And Row
% CNR = sqrt(IPS);
% % Get the number of subplot is need: Number of Subplot
% NOS = ceil(length(all_data)/IPS);
% 
% 
% % Initiating subplot
% % For each figure
% for FN = 1:NOS
%     figure
%     %Determin the cell index on the subplot
%     if length(all_data) >= IPS*FN
%         CI = 1:IPS;
%     elseif length(all_data) < IPS*FN
%         CI = 1:(length(all_data)-IPS*(FN-1));
%     end
%     
%     for i_CI = CI
%         subplot(CNR,CNR,i_CI);
%         %Get the Current Cell Index
%         CCI = (FN-1)*IPS + i_CI;
%         %Get the end frame of cell lifespan
%         life_end = all_data(CCI).cycle(end);
%         %Get the start frame of cell lifespan
%         life_start = all_data(CCI).cycle(3);
%         %Get the frames of lifespan for index fluorescence
%         FLS = life_start:life_end;
%         %Get the cell cycle info
%         cycles = all_data(CCI).cycle(3:end);
%         %Remove the zeros
%         cycles = cycles(cycles>0);
%   
%         %Extract the curr_traj info and smooth it within 6 window
%         curr_trace_Flu = all_data(CCI).traj_normalized(FLS,:,Flu(1));
%         curr_trace_End = all_data(CCI).traj_normalized(FLS,:,Flu(2));
%         
%         %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%         %%%%%%% To convert the unit of x axis from frames to minius %%%%%%%
%         date = all_data(CCI).Date;
%         date = num2str(date);
%         if strcmp(date,'20151112')
%             FLS = 6*FLS;
%             curr_trace_Flu = smooth(curr_trace_Flu,30);
%             curr_trace_End = smooth(curr_trace_End,30);
%             cycles2 = 6*cycles;
%         else
%             FLS = 15*FLS;
%             curr_trace_Flu = smooth(curr_trace_Flu,12);
%             curr_trace_End = smooth(curr_trace_End,12);
%             cycles2 = 15*cycles;
%         end
%         %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 
%     
%         %Plot Fluorescence channel and the Nuclear marker Channel
%         [hAx,hl1,hl2] = plotyy(FLS,curr_trace_Flu,FLS,curr_trace_End);
%         
%         box off
%         
%         %Set up the properties of 1st axis
%         hAx(1).YLim = [0 3];        
%         hAx(1).YTickMode = 'auto';
%         hAx(1).XLim = [0 6*max_x];%% use 6 min interval or 15 min interal depend on the data
%         hl1.LineWidth = 1.5;
%         hAx(1).YColor = 'blue';
%         hl1.Color = 'blue';
%         ylabel(hAx(1),Label);
%         
%         
%         %Set up the properties of 2nd axis
%         hAx(2).YLim = [0 3];
%         hAx(2).YTickMode = 'auto';
%         hAx(2).XLim = [0 6*max_x];
%         hl2.LineWidth = 1.5;
%         hAx(2).YColor = 'red';
%         hl2.Color = 'red';
%         ylabel(hAx(2),'Nhp6a-iRFP');
% 
%         xlabel(hAx(1),'Time (min)');
%        
%         cell_title = [num2str(all_data(CCI).age) ',',all_data(CCI).id, ',',num2str(all_data(CCI).Date),',','DT', num2str(all_data(CCI).Death_type)];
%         
%         title(cell_title);
%         
%         %Add the cell cycle line
%         y1 = get(gca,'ylim');
%         for k_y = cycles2
%             line([k_y k_y],y1,'Color','k','LineStyle','--','LineWidth',1.5)
%         end
%         set(gca,'FontSize',12)
%         
%     end
%     
% % % % % % % %     [ax,h3]=suplabel('NTS1-pGPD-GFP' ,'t'); 
% % % % % % % %     set(h3,'FontSize',20)
%    
% end
%