PlotPhasePrecession

PlotPhasePrecession - Plot phase precession plots and maps.

  USAGE

    PlotPhasePrecession(data,stats,<options>)

    data           phase precession data obtained using <a href="matlab:help PhasePrecession">PhasePrecession</a>
    stats          optional phase precession stats obtained using <a href="matlab:help PhasePrecession">PhasePrecession</a>
    <options>      optional list of property-value pairs (see table below)

    =========================================================================
     Properties    Values
    -------------------------------------------------------------------------
     'smooth'      size in bins of the smoothing kernel for the phase map
                   (0 = no smoothing, default = 4)
     'nBins'       number of x and phase bins (default = [100 100])
     'track'       'linear' or 'circular' (default = 'linear')
     'laps'        plot all laps together ('all', default) or separately
                   ('single')
     'parent'      parent figure or uipanel handle (default = gcf)
    =========================================================================

  SEE

    See also PhasePrecession.

0001 function PlotPhasePrecession(data,stats,varargin)
0002 
0003 %PlotPhasePrecession - Plot phase precession plots and maps.
0004 %
0005 %  USAGE
0006 %
0007 %    PlotPhasePrecession(data,stats,<options>)
0008 %
0009 %    data           phase precession data obtained using <a href="matlab:help PhasePrecession">PhasePrecession</a>
0010 %    stats          optional phase precession stats obtained using <a href="matlab:help PhasePrecession">PhasePrecession</a>
0011 %    <options>      optional list of property-value pairs (see table below)
0012 %
0013 %    =========================================================================
0014 %     Properties    Values
0015 %    -------------------------------------------------------------------------
0016 %     'smooth'      size in bins of the smoothing kernel for the phase map
0017 %                   (0 = no smoothing, default = 4)
0018 %     'nBins'       number of x and phase bins (default = [100 100])
0019 %     'track'       'linear' or 'circular' (default = 'linear')
0020 %     'laps'        plot all laps together ('all', default) or separately
0021 %                   ('single')
0022 %     'parent'      parent figure or uipanel handle (default = gcf)
0023 %    =========================================================================
0024 %
0025 %  SEE
0026 %
0027 %    See also PhasePrecession.
0028 
0029 % Copyright (C) 2009-2012 by Michaël Zugaro
0030 %
0031 % This program is free software; you can redistribute it and/or modify
0032 % it under the terms of the GNU General Public License as published by
0033 % the Free Software Foundation; either version 3 of the License, or
0034 % (at your option) any later version.
0035 
0036 % Default values
0037 track = 'linear';
0038 nBins = [100 100];
0039 smooth = 4;
0040 parent = [];
0041 laps = 'all';
0042 
0043 % Check number of parameters
0044 if nargin < 1,
0045   error('Incorrect number of parameters (type ''help <a href="matlab:help PlotPhasePrecession">PlotPhasePrecession</a>'' for details).');
0046 end
0047 
0048 if nargin > 1 && ~isstruct(stats),
0049     varargin = {stats varargin{:}};
0050     stats = [];
0051 end
0052 
0053 % Parse parameter list
0054 for i = 1:2:length(varargin),
0055     if ~ischar(varargin{i}),
0056         error(['Parameter ' num2str(i+2) ' is not a property (type ''help <a href="matlab:help PlotPhasePrecession">PlotPhasePrecession</a>'' for details).']);
0057     end
0058     switch(lower(varargin{i})),
0059         case 'smooth',
0060             smooth = varargin{i+1};
0061             if ~isdscalar(smooth,'>0'),
0062                 error('Incorrect value for property ''smooth'' (type ''help <a href="matlab:help PlotPhasePrecession">PlotPhasePrecession</a>'' for details).');
0063             end
0064         case 'nbins',
0065             nBins = varargin{i+1};
0066             if ~isivector(nBins,'>0','#2'),
0067                 error('Incorrect value for property ''nBins'' (type ''help <a href="matlab:help PlotPhasePrecession">PlotPhasePrecession</a>'' for details).');
0068             end
0069         case 'track',
0070             track = lower(varargin{i+1});
0071             if ~isastring(track,'linear','circular'),
0072                 error('Incorrect value for property ''track'' (type ''help <a href="matlab:help PlotPhasePrecession">PlotPhasePrecession</a>'' for details).');
0073             end
0074         case 'laps',
0075             laps = lower(varargin{i+1});
0076             if ~isastring(laps,'all','single'),
0077                 error('Incorrect value for property ''laps'' (type ''help <a href="matlab:help PlotPhasePrecession">PlotPhasePrecession</a>'' for details).');
0078             end
0079         case 'parent',
0080             parent = varargin{i+1};
0081             if ~ishandle(parent),
0082                 error('Incorrect value for property ''parent'' (type ''help <a href="matlab:help PlotPhasePrecession">PlotPhasePrecession</a>'' for details).');
0083             end
0084         otherwise,
0085             error(['Unknown property ''' num2str(varargin{i}) ''' (type ''help <a href="matlab:help PlotPhasePrecession">PlotPhasePrecession</a>'' for details).']);
0086     end
0087 end
0088 
0089 if isempty(parent), parent = gcf; end
0090 if strcmp(track,'linear'),
0091     curveType = 'll';
0092 else
0093     curveType = 'cl';
0094 end
0095 
0096 % Initialize a few variables
0097 t = data.position.t;
0098 x = data.position.x;
0099 pp = data.position.phase;
0100 l = data.position.lap;
0101 r = data.rate.r;
0102 pr = data.rate.phase;
0103 nBinsX = nBins(1);
0104 nBinsP = nBins(2);
0105 
0106 if strcmp(laps,'all'),
0107 
0108     % Rate vs position plot
0109     a = subplot(4,1,1,'parent',parent);
0110     nBins = 200;
0111     curve = FiringCurve(data.x,t,'nbins',nBins,'smooth',2,'type',curveType);
0112     if strcmp(track,'linear'),
0113         plot(curve.x,curve.rate,'b');
0114         xlim([0 1]);
0115     else
0116         plot([curve.x curve.x+1],[curve.rate curve.rate],'b');
0117         xlim([0 2]);
0118     end
0119     set(a,'tickdir','out');
0120     ylabel('Firing Rate (Hz)');
0121 
0122     % Phase vs position plot
0123     a = subplot(4,1,2,'parent',parent);
0124     if strcmp(track,'linear'),
0125         plot([x;x],[pp;pp+2*pi]*180/pi,'k.','markersize',4);
0126         if ~isempty(stats) && ~isempty(stats.slope),
0127             hold on;
0128             dx = max(x)-min(x);
0129             xm = mean([min(x);max(x)]);
0130             ym = wrap(stats.slope*xm+stats.intercept,2)*180/pi;
0131             PlotSlope(xm,ym,stats.slope*180/pi,dx,'r');
0132             PlotSlope(xm,ym+360,stats.slope*180/pi,dx,'r');
0133         end
0134         xlim([0 1]);
0135     else
0136         plot([x;x;x+1;x+1],[pp;pp+2*pi;pp;pp+2*pi]*180/pi,'k.','markersize',4);
0137         if ~isempty(stats) && ~isempty(stats.slope),
0138             hold on;
0139             if diff(stats.boundaries) < 0,
0140                 % Field wraps around boundaries
0141                 % (we use the right portion of the field as a 'reference' and shift the left portion
0142                 % accordingly, therefore the intercept can be used as is - see PhasePrecession)
0143                 fieldStart = stats.boundaries(1);
0144                 fieldStop = max(x)+stats.boundaries(2);
0145             else
0146                 fieldStart = min(x);
0147                 fieldStop = max(x);
0148             end
0149             dx = fieldStop - fieldStart;
0150             xm = mean([fieldStop fieldStart]);
0151             ym = wrap(stats.slope*xm+stats.intercept,2)*180/pi;
0152             PlotSlope(xm,ym,stats.slope*180/pi,dx,'r');
0153             PlotSlope(xm,ym+360,stats.slope*180/pi,dx,'r');
0154             PlotSlope(xm+1,ym,stats.slope*180/pi,dx,'r');
0155             PlotSlope(xm+1,ym+360,stats.slope*180/pi,dx,'r');
0156         end
0157         xlim([0 2]);
0158     end
0159     set(a,'ytick',0:90:720,'ylim',[0 720],'tickdir','out');
0160     ylabel('Phase (°)');
0161 
0162     % Phase vs position map
0163     a = subplot(4,1,3,'parent',parent);
0164     x0 = Bin(x,[0 1],nBinsX);
0165     p0 = Bin(pp,[0 2*pi],nBinsP);
0166     map = Accumulate([p0 x0],1,[nBinsP nBinsX]);
0167     if strcmp(track,'linear'),
0168         map = [map;map];
0169         map = Smooth(map,2);
0170         PlotColorMap(map,1,'x',linspace(0,1,nBinsX+1),'y',0:6:720);
0171     else
0172         map = [map map;map map];
0173         map = Smooth(map,smooth);
0174         PlotColorMap(map,1,'x',linspace(0,2,2*nBinsX+1),'y',0:6:720);
0175     end
0176     set(a,'ytick',0:90:720,'ylim',[0 720],'tickdir','out','ydir','normal');
0177     xlabel('Position');
0178     ylabel('Phase (°)');
0179 
0180     % Phase vs rate plot
0181     a = subplot(4,1,4,'parent',parent);
0182     if isempty(r), return; end
0183     rnd = randn(size(r))/5; % jitter points horizontally
0184     plot(r+rnd,pr*180/pi,'k.','markersize',4);
0185     hold on;
0186     n = max(r);
0187     for i = 1:n,
0188         if any(r==i),
0189             [m(i,1),c(i,:)] = CircularConfidenceIntervals(pr(r==i));
0190         else
0191             m(i,1) = NaN;
0192             c(i,1:2) = NaN;
0193         end
0194     end
0195     neg = m<0;
0196     m(neg) = m(neg)+2*pi;
0197     c(neg,:) = c(neg,:)+2*pi;
0198     m = m*180/pi;
0199     c = c*180/pi;
0200     errorbar(1:n,m,m-c(:,2),c(:,1)-m,'r');
0201     set(a,'ytick',0:90:360,'ylim',[0 360],'tickdir','out');
0202     xlabel('Firing Rate (spikes / 2 cycles)');
0203     ylabel('Phase (°)');
0204 
0205 else % Plot laps separately
0206 
0207     colors = 'bk';
0208 
0209     % List and count lap numbers
0210     laps = unique(data.position.lap);
0211     laps = laps(laps~=0);
0212     nLaps = length(laps);
0213 
0214     % Rate vs position plot
0215     a = subplot(2,1,1,'parent',parent);
0216     hold on;
0217     nBins = 200;
0218     curve = FiringCurve(data.x,t,'nbins',nBins,'smooth',2,'type',curveType);
0219     for i = 1:nLaps,
0220         style = colors(mod(i,2)+1);
0221         if strcmp(track,'linear'),
0222             plot(curve.x+(i-1),curve.rate,style,'markersize',4);
0223             xlim([0 nLaps]);
0224         else
0225             plot([curve.x curve.x+1]+2*(i-1),[curve.rate curve.rate],style,'markersize',4);
0226             xlim([0 2*nLaps]);
0227         end
0228     end
0229     set(a,'tickdir','out','xtick',1:nLaps,'xticklabel',[]);
0230     xlabel('Position');
0231     ylabel('Firing Rate (Hz)');
0232 
0233     % Phase vs position plot
0234     a = subplot(2,1,2,'parent',parent);
0235     hold on;
0236     for i = 1:nLaps,
0237         style = [colors(mod(i,2)+1) '.'];
0238         if strcmp(track,'linear'),
0239             plot([x(l==i);x(l==i)]+(i-1),[pp(l==i);pp(l==i)+2*pi]*180/pi,style,'markersize',4);
0240             if ~isempty(stats) && ~isempty(stats.slope),
0241                 hold on;
0242                 dx = max(x(l==i))-min(x(l==i));
0243                 xm = mean([min(x(l==i));max(x(l==i))])+(i-1);
0244                 ym = wrap(stats.lap.slope(i)*xm+stats.lap.intercept(i),2)*180/pi;
0245                 PlotSlope(xm,ym,stats.lap.slope(i)*180/pi,dx,'r');
0246                 PlotSlope(xm,ym+360,stats.lap.slope(i)*180/pi,dx,'r');
0247             end
0248             xlim([0 nLaps]);
0249         else
0250             plot([x(l==i);x(l==i);x(l==i)+1;x(l==i)+1]+2*(i-1),[pp(l==i);pp(l==i)+2*pi;pp(l==i);pp(l==i)+2*pi]*180/pi,style,'markersize',4);
0251             if ~isempty(stats) && ~isempty(stats.slope),
0252                 hold on;
0253                 dx = max(x(l==i))-min(x(l==i));
0254                 xm = mean([min(x(l==i));max(x(l==i))]);
0255                 ym = wrap(stats.lap.slope(i)*xm+stats.lap.intercept(i),2)*180/pi;
0256                 PlotSlope(xm+2*(i-1),ym,stats.lap.slope(i)*180/pi,dx,'r');
0257                 PlotSlope(xm+2*(i-1),ym+360,stats.lap.slope(i)*180/pi,dx,'r');
0258                 PlotSlope(xm+1+2*(i-1),ym,stats.lap.slope(i)*180/pi,dx,'r');
0259                 PlotSlope(xm+1+2*(i-1),ym+360,stats.lap.slope(i)*180/pi,dx,'r');
0260             end
0261             xlim([0 2*nLaps]);
0262         end
0263     end
0264     set(a,'ytick',0:90:720,'ylim',[0 720],'tickdir','out','xtick',1:nLaps,'xticklabel',[]);
0265     xlabel('Position');
0266     ylabel('Phase (°)');
0267 
0268 end