%%%  The order of file names should be consistent.  The first and second
%%%  files will be plotted against each other and the third and fourth files
%%%  will be plotted againast each other.  Furthermore 1 and 3 should match
%%%  and 2 and 4 should match. For example in the below example 1 and 3 are
%%%  both V2 and 2 and 4 are both V5.  These will need to match to ensure
%%%  that the same variable type is ploted on the same axes.
%%%  Also, you will need to be in the same directory as these files for
%%%  this script to run.
%%%
%%%  To use this script, open the file with the matlab editor. Change the
%%%  file names to match your own (paying attention to the rules mentioned
%%%  above.  Make sure you are in the same directory as the files and then
%%%  simply hit crtl+enter on windows and linux, or command+enter on OS X.
%%%  This will run the script and generate the figure for you.
%%%
%%% Example:
%%% filenames = {'PPI_V2xAtn.mat' 'PPI_V5xAtn.mat' 'PPI_V2xNoAtn.mat' 'PPI_V5xNoAtn.mat'};
%%%
%%%
%%% Enjoy!,  Aaron Schultz 03-16-2010, aschultz@nmr.mgh.harvard.edu
%%%
%%%

filenames = {'PPI_V2xAtn.mat' 'PPI_V5xAtn.mat' 'PPI_V2xNoAtn.mat' 'PPI_V5xNoAtn.mat'};

for ii = 1:length(filenames);
    fn = filenames{ii};
    ind = find(fn == '.');
    name = fn(1:ind-1);
    load(fn);
    dat(:,ii) = PPI.ppi;
    
    ind = find(fn=='_');
    filenames{ii}(ind) = '-';
end

figure(1); clf; 
 
plot(dat(:,1), dat(:,2),'k.', 'markersize', 6); 
hold on; 
plot(dat(:,3), dat(:,4),'r.', 'markersize', 6); shg
plot(dat(:,1), polyval(polyfit(dat(:,1), dat(:,2),1) , dat(:,1)),'k-', 'linewidth', 1.5); shg
plot(dat(:,3), polyval(polyfit(dat(:,3), dat(:,4),1) , dat(:,3)),'r-', 'linewidth', 1.5); shg

a = legend([filenames{1} ' vs. ' filenames{2}], [filenames{3} ' vs. ' filenames{4}]);
set(a,'Fontsize', 14, 'location', 'NorthWest');

xlabel('Whatever Type Filename #1 is.', 'fontsize', 14);
ylabel('Whatever Type Filename #2 is.', 'fontsize', 14);

title('A title', 'fontsize', 16, 'fontname', 'Times');