clear all; 
close all; 
clc

%%

%%% place the name of the file here
filename = 'Hemocytometer_Data_Final.xlsx';

x_tg = [2 4 7 9 11 15 16 18 21 23 25 28 30 32 35 37 39 42]; % the x axis is the growth time in days 

%%%%%%%% read the cell number from excel sheet %%%
Flask_1 = xlsread(filename,1,'L2:L19'); % 1 indicates the sheet number for 'Graph', please tune the range 
Flask_2 = xlsread(filename,1,'L20:L37'); 
Flask_3 = xlsread(filename,1,'L38:L55');  
Flask_4 = xlsread(filename,1,'L56:L73');  
Flask_5 = xlsread(filename,1,'L74:L91');  
Flask_6 = xlsread(filename,1,'L92:L109');  
Flask_7 = xlsread(filename,1,'L110:L127');  
Flask_8 = xlsread(filename,1,'L128:L145'); 
Flask_9 = xlsread(filename,1,'L146:L163');  
Flask_10 = xlsread(filename,1,'L164:L181'); 

%%%%%%%% Calculate the mean and standard error for each sceneria %%%%% 

%%%% cell density %%%% (cells/mm^3)
y_woclay_mean = mean([Flask_2,Flask_5,Flask_8],2);
y_woclay_sem = std([Flask_2,Flask_5,Flask_8],0,2)./sqrt(3); %standard error of mean

y_clay_mean = mean([Flask_3,Flask_6,Flask_9],2);
y_clay_sem = std([Flask_3,Flask_6,Flask_9],0,2)./sqrt(3);

y_claymodified_mean = mean([Flask_4,Flask_7,Flask_10],2);
y_claymodified_sem = std([Flask_4,Flask_7,Flask_10],0,2)./sqrt(3);

    
     %% Read C_cell vs time
    h_p2_2 = figure; hold on
    set(gca,'fontsize',18,'fontweight','bold');
    
    herr = errorbar(x_tg, y_woclay_mean,y_woclay_sem) %,'o','MarkerSize',9,'linewidth',2)
%     set(herr(1),'color','b','Marker','.','linewidth',2)
    set(herr,'color','b','LineStyle','-','Marker','o','MarkerSize',9,'linewidth',2)
    
    herr3 = errorbar(x_tg, y_claymodified_mean,y_claymodified_sem) %,'o','MarkerSize',9,'linewidth',2)
%     set(herr(1),'color','b','Marker','.','linewidth',2)
    set(herr3,'color','g','LineStyle','-','Marker','o','MarkerSize',9,'linewidth',2)
    
    
    herr2 = errorbar(x_tg, y_clay_mean,y_clay_sem) %,'o','MarkerSize',9,'linewidth',2)
%     set(herr(1),'color','b','Marker','.','linewidth',2)
    set(herr2,'color','r','LineStyle','-','Marker','s','MarkerSize',9,'linewidth',2)
    
    
    xlabel('t_g [days]')
    ylabel('C_{cell} [10^7/mL]')
    
    legend('Pure solution','Solution modified by clay','With 1% clay','location','northwest');
    legend boxoff
    
    
    box on 
%     title('C_{cell} vs Growth time')
    
    set(h_p2_2,'PaperPositionMode','Manual')
    set(h_p2_2,'PaperUnits','inches')
    set(h_p2_2,'PaperSize',[8 6.1])
    set(h_p2_2,'PaperPosition',[0 0.1 8 6])
    saveas(h_p2_2, ['C_cell_vs_tg_Katherine_Fall2021'], 'pdf')