%% Preliminaries:

close all; clear all;
load('MakeStackHistData.mat')

%% Define the bins to use for our data (you will need to adjust this depending on your data):

%In this case we are using the same bins for each data set.  You probably
%want to do this when you are plotting stacked histograms.

bins=logspace(0,4,60);
x=bins;

%% Bin your data using Matlabs "hist" function.  

%The variable "n" will be the number in each bin described by the variable
%"x".  HistData will become a matrix of the normalized bins (normalized to
%the total number of elements).  Means will become a vector of the mean
%value for each distribution, which we will use when coloring our
%histograms (so that colors roughly correspond to the mean of the
%distribution).

HistData=[];  
Means=[];

for i=1:5
    [n,x]=hist(Data(i,:),x);
    HistData=[HistData; n./sum(n)];
    Means=[Means mean(Data(i,:))];
end



%% Define a colormap for the histograms that will make the histograms brighter as the mean of the distribution increases

% In this case we chose to make the histograms brighter green at higher
% mean values since the flow cytometry data is of GFP.
 
%Define a color map
MMColorMap=zeros(5,3);

%Define colors so that they scale with the difference between the mean
%fluorescence at a given timepoint and the mean at time 0


MM=sort(Means);
MMdiff=Means-Means(1);
MMdiff=MMdiff./(max(MMdiff));


MMColorMap(1:end,2)=MMdiff;

%Set up the figure and axis properties:
h=figure; hold; colors=colormap;

set(gca,'XScale','log')
set(gca,'XLim',[10,2000])
set(gca,'PlotBoxAspectRatioMode','manual')
set(gca,'PlotBoxAspectRatio',[1 3 1])
set(gca,'FontSize',12)
set(gca,'XTick',[100 1000 10000 100000])
set(gca,'YTick',[0 1])
ylabel('Fraction of Cell Population','FontSize',14)
xlabel('Fluorescence [a.u.]','FontSize',14)

%% Plot the histograms along the y-axis

spacing=.15;  %Spacing along the y-axis chosen empirically 

for i=1:5
    fill([x(1);x'; x'],[i*spacing; (HistData(i,:)+i*spacing)'; ones(1,length(x))'*i*spacing],MMColorMap(i,:),'LineStyle','none')
    semilogx(x,HistData(i,:)+i*spacing,'LineWidth',3,'Color','k');
end


%% Save the histogram figure
saveas(h,'ExampleStackedHistograms','fig')
saveas(h,'ExampleStackedHistograms','png')
saveas(h,'ExampleStackedHistograms','ai')
saveas(h,'ExampleStackedHistograms','pdf')