McClean: FindGates.m

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function [Gates,FNames]=FindGate(filenameORdata, varargin) % function [Gates,FNames]=FindGate(filenameORdata, varargin) % SUMMARY: % % This function takes a filename (or part of name) of a .fcs file (or several files) OR the data from the .fcs % file (see below), lets the user select a gate from a plot of the % side-scatter vs the forward scatter and returns the indices of the data % points in the fcs data that are within this gate. % % INPUTS: % filenameORdata: This is either the name of a single .fcs file to open, a % string that when used with dir will return several .fcs files (ie % '*177*'), or the actual fcs FACS data (ie fcsdat from the call to % [fcsdat, fcshdr] = fca_readfcs(filename)) % % varargin: % varargin{1}: 0 if output is to be suppressed (default), 1 if output % (ie, plot of the gate and the stuff in the gate) IS to be plotted % varargin{2}: name for the title of the plot when data is sent in rather % than a filename % % % OUTPUTS: % Gate: A cell array, each entry is the indices of the points that fall within the user-defined % polygon for a given .fcs file. In later functions, in order to just use these points you % would do the following: (Say you just wanted the GFP data for these points, and GFP is % the third column of fcsdat from the call [fcsdat, fcshdr] = fca_readfcs(filename)) % use fcsdat(Gates{i},3) where you want the gates for the ith file. % % FNames: A cell array with the names of the files that the gates belong % to (for data, assume user gave the appropriate filename), so Gates{i} % is the gate information for .fcs file FNames{i} % % % REQUIRES: % fca_readfcs % % REFERENCES: % Mathworks documentation on inpolygon: % http://www.mathworks.com/help/techdoc/ref/inpolygon.html % % Written by Megan McClean, Ph.D. % Lewis-Sigler Institute for Integrative Genomics % Princeton University % 120 Carl Icahn % Princeton, NJ 08544 % mmcclean@princeton.edu % % Last revised on February 22, 2012



%% numarg=length(varargin); Gates={};

%% %Read in the data from the .fcs file using fca_readfcs or get the list of %files represented by the substring filenameORdata if ischar(filenameORdata)

   files=dir(filenameORdata);
   %If the user entered a filename, open that file and use it as the data
   for j=1:length(files)
       [fcsdat, fcshdr] = fca_readfcs(files(j).name);
       figure; hold;
       plot(fcsdat(:,1), fcsdat(:,2), '.')
       xlabel('FSC-A'); ylabel('SSA-A'); title(fcshdr.filename);


       %Get user input for the vertices of polygon surrounding the region of
       %interest
       [x,y]=ginput();
       %set up the polygon surrounding the points you want:
       x=[x; x(1)];
       y=[y; y(1)];
       InGate=inpolygon(fcsdat(:,1), fcsdat(:,2), x,y);
       Gates{j}=InGate;


       %display what points are in the polygon
       if numarg>0
           if varargin{1}==1
               plot(fcsdat(InGate,1), fcsdat(InGate,2),'ro')
               legend('All Points', 'Points within user-defined gate');
               pause; close all;
           else
               close all;
           end
       else
           close all;
       end
       FNames{j}=files(j).name;
   end

else

   %If the user just sent in a variable, then use the data in that
   %variable
   fcsdat=filenameORdata;
   numarg=length(varargin);
   if numarg<2
       fcshdr.filename='Unlabelled Data--Need to Edit Title';
   else
       fcshdr.filename=varargin(2);
   end
     FNames{1}=fcshdr.filename;
   %We are going to assume that the data in fcsdat is formatted so that forward scatter
   %(FSC-A) is the first column and side scatter (SSA-A) is in the second
   %column
   figure; hold;
   plot(fcsdat(:,1), fcsdat(:,2), '.')
   xlabel('FSC-A'); ylabel('SSA-A'); title(fcshdr.filename);


   %Get user input for the vertices of polygon surrounding the region of
   %interest
   [x,y]=ginput();


   %set up the polygon surrounding the points you want:
   x=[x; x(1)];
   y=[y; y(1)];
   InGate=inpolygon(fcsdat(:,1), fcsdat(:,2), x,y);
   Gates{1}=InGate;


   %display what points are in the polygon
   if numarg>0
       if varargin{1}==1
           plot(fcsdat(InGate,1), fcsdat(InGate,2),'ro');
           pause;
           legend('All Points', 'Points within user-defined gate');
           close all;
       else
           close all;
       end
   else
       close all;
   end
 

end close all;