gateHistDen

 gateHistDen : makes a probability density plot for the list of cells
 in the clist table for the given clist index.
 It first gates the list if there is a gate field in clist.

 INPUT :
   clist : list of cells with time-independent info
   ind : indices of clist definition used for x and y label [x,y]
   xx : array of two values, the subtraction of which is the size of each bin.
   cc : color of plot
 OUTPUT :
   y : probability density
   xx : values of clist(ind)


 Copyright (C) 2016 Wiggins Lab
 Written by Paul Wiggins.
 University of Washington, 2016
 This file is part of SuperSegger.

 SuperSegger is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.

 SuperSegger is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.

 You should have received a copy of the GNU General Public License
 along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.

0001 function [y,xx] = gateHistDen(clist, ind, cc,xx)
0002 % gateHistDen : makes a probability density plot for the list of cells
0003 % in the clist table for the given clist index.
0004 % It first gates the list if there is a gate field in clist.
0005 %
0006 % INPUT :
0007 %   clist : list of cells with time-independent info
0008 %   ind : indices of clist definition used for x and y label [x,y]
0009 %   xx : array of two values, the subtraction of which is the size of each bin.
0010 %   cc : color of plot
0011 % OUTPUT :
0012 %   y : probability density
0013 %   xx : values of clist(ind)
0014 %
0015 %
0016 % Copyright (C) 2016 Wiggins Lab
0017 % Written by Paul Wiggins.
0018 % University of Washington, 2016
0019 % This file is part of SuperSegger.
0020 %
0021 % SuperSegger is free software: you can redistribute it and/or modify
0022 % it under the terms of the GNU General Public License as published by
0023 % the Free Software Foundation, either version 3 of the License, or
0024 % (at your option) any later version.
0025 %
0026 % SuperSegger is distributed in the hope that it will be useful,
0027 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0028 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0029 % GNU General Public License for more details.
0030 %
0031 % You should have received a copy of the GNU General Public License
0032 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0033 
0034 clist = gate(clist);
0035 ss = size( clist.data );
0036 NUM_CELLS = ss(1);
0037 NUM_BINS = round(sqrt(NUM_CELLS));
0038 
0039 if ~exist( 'xx', 'var' )
0040     xx = [];
0041 else
0042     dx = xx(2) - xx(1);
0043     start = min(clist.data(:,ind));
0044     stop = max(clist.data(:,ind));
0045     xx = start:dx:stop;
0046 end
0047 
0048 if ~exist( 'cc', 'var' ) || isempty(cc)
0049     cc = 'b';
0050 end
0051 
0052 
0053 nind = numel( ind );
0054 
0055 if nind == 1
0056     if isempty( xx )
0057         [y,xx] = hist(clist.data(:,ind), NUM_BINS );
0058     else
0059         [y,xx] = hist(clist.data(:,ind), xx );
0060     end
0061     
0062     dx = xx(2)-xx(1);
0063     plot( xx, y/dx/NUM_CELLS, '.-', 'Color', cc );
0064     tmp = ishold;
0065     hold on
0066     plot( mean(clist.data(:,ind))+[0,0], [max(y),min(y(y>0))]/dx/NUM_CELLS, ':', 'Color', cc );
0067     
0068     if ~tmp
0069         hold off;
0070     end
0071     
0072     ylabel('Population Density');
0073     xlabel(clist.def{ind});
0074 else
0075     disp('Error in getHist: too many indices in ind');
0076 end
0077 
0078 
0079 
0080 end