pop_tesa_plot.m

% pop_tesa_plot() - plots TMS-evoked activity averaged over trials. Timing of
%               the TMS pulse is indicated with a red dashed line. Output
%               from peak analyses can also be plotted as well as
%               confidence intervals across trials.
%
% Usage:
%   >>  pop_tesa_plot( EEG ); % pop up window
%   >>  pop_tesa_plot( EEG, 'key1',value1... );
%
% Inputs:
%   EEG             - EEGLAB EEG structure
% 
% Optional input pairs:
%   'xlim', [min,max] - integers describing the x axis limits in ms.
%                   default = [-100,500]
%   'ylim', [min,max] - integers describing the y axis limits in ms. If
%                   left blank, the plot will automatically scale.
%                   default = []
%                   Examples: [-10,10]
%   'elec','str'  - string describing a single electrode  
%                   for plotting. If left blank, a butterfly plot of all electrodes 
%                   will be plotted.
%                   default = [];
%                   Example: 'Cz'
%   'CI','str'      - 'on' | 'off'. Plot confidence interval calculated
%                   across trials. This option is not available for GMFA
%                   and butterfly plots.
%                   default = 'off';
%   
% Options for plotting output from tesa_tepextract and tesa_peakanalysis
%   'tepType','str'  - 'data' | 'ROI' | 'GMFA'. 'Data' input extracts data
%                   for plotting from EEG.data. 'ROI' input selects a ROI
%                   generated by tesa_tepextract. 'GMFA' input selects a
%                   GMFA generated by tesa_tepextract. Note that if
%                   multiple ROIs or GMFAs are present, 'tepName' must also
%                   be included to determine which one to plot.
%                   Default = 'data';
%   'tepName', 'str' - String is either the name of a ROI or GMFA generated
%                   by tesa_tepextract. The default names generated by
%                   tesa_tepextract are 'R1','R2'... etc. however the user
%                   can also define names. This is required if multiple ROIs or GMFAs are present. 
%                   Default = []; 
%   'plotPeak','str' - 'off' | 'on'. If 'on', peaks identified with
%                   tesa_peakanalysis will also be plotted. A box defining
%                   the lower and upper time limits in which the peak was
%                   searched will also be plotted. Green indiciates that a
%                   peak was found, red a peak was not detected. Note that
%                   tesa_peakanalysis must be run prior to using this
%                   function and 'tepType' must also be called.
% 
% Examples:
%   pop_tesa_plot(EEG, 'xlim', [-200,600], 'ylim', [-10,10], 'elec', 'P1', 'CI', 'on'); % plot electrode P1, rescale the axes and include confidence intervals.
%   pop_tesa_plot(EEG, 'tepType','ROI','tepName','parietal','plotPeak','on','CI','on'); % plot the output from a ROI analysis called parietal including detected peaks and confidence intervals
%   pop_tesa_plot(EEG, 'tepType','GMFA','plotPeak','on'); % plot output from a GMFA analysis including detected peaks
% 
% See also:
%   tesa_tepextract, tesa_peakanalysis, tesa_peakoutput 

% Copyright (C) 2016  Nigel Rogasch, Monash University,
% nigel.rogasch@monash.edu
%
% This program 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 2 of the License, or
% (at your option) any later version.
%
% This program 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 this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 function com = pop_tesa_plot( EEG, varargin )

com = '';          

%check that data is present
if isempty(EEG.data)
    error('Data is empty');
end

% pop up window
% -------------
if nargin < 2
    
    chanAll = {EEG.chanlocs.labels};
    
   if isfield(EEG,'ROI')
        roiFields = fieldnames(EEG.ROI);
        roi = 'yes';
        for a = 1:size(roiFields,1)
            roiFields{a,1} = ['ROI ',roiFields{a,1}];
        end
    else 
        roi = 'no';
    end
    if isfield(EEG,'GMFA')
        gmfaFields = fieldnames(EEG.GMFA);
        gmfa = 'yes';
        for a = 1:size(gmfaFields,1)
            gmfaFields{a,1} = ['GMFA ',gmfaFields{a,1}];
        end
    else 
        gmfa = 'no';
    end

    if strcmpi(roi,'yes') && strcmpi(gmfa,'yes')
        tepInput = ['All', chanAll, roiFields', gmfaFields'];
    elseif strcmpi(roi,'yes') && strcmpi(gmfa,'no')
        tepInput = ['All', chanAll, roiFields'];
    elseif strcmpi(roi,'no') && strcmpi(gmfa,'yes')
        tepInput = ['All', chanAll, gmfaFields'];
    elseif strcmpi(roi,'no') && strcmpi(gmfa,'no')
        tepInput = ['All', chanAll];
    end
    
    tepAll = tepInput;
    
    for a = 1:size(tepInput,1)-1
        tepInput{a,1} = [tepInput{a,1},'|'];
    end
    
    geometry = {1 [0.5 0.5] 1 1 [1 0.5] [1 0.5] 1 [1 0.5] 1 1 1 [1 0.5]};

    uilist = {{'style', 'text', 'string', 'Plot TMS-evoked potentials','fontweight','bold'} ...
              {'style', 'text', 'string', 'Data to plot'} ...
              {'style', 'popupmenu', 'string', tepInput 'tag' 'data' } ...
              {}...
              {'style', 'text', 'string', 'Plot options','fontweight','bold'} ...
              {'style', 'text', 'string', 'Time limits (ms) (e.g. -100,500)'} ...
              {'style', 'edit', 'string', '-100,500'} ...
              {'style', 'text', 'string', 'Amplitude limits (uV) (e.g. -30,30)'} ...
              {'style', 'edit', 'string', ''}...
              {'style', 'text', 'string', '   Leave empty for auto-scale', 'fontangle','italic'} ...
              {'style', 'text', 'string', 'Plot confidence interval',} ...
              {'Style', 'checkbox', 'string' 'on/off' 'value' 0 'tag' 'CI' }...
              {'style', 'text', 'string', '   Single electrode and ROI only','fontangle','italic'}...
              {} ...
              {'style', 'text', 'string', 'For analysed data (ROI, GMFA)','fontweight','bold'} ....
              {'style', 'text', 'string', 'Plot peak analysis results',} ...
              {'Style', 'checkbox', 'string' 'on/off' 'value' 0 'tag' 'peaks' } ...
              };
             
    result = inputgui('geometry', geometry, 'uilist', uilist, 'title', 'Plot TEPs -- pop_tesa_plot()', 'helpcom', 'pophelp(''pop_tesa_plot'')');
    if isempty(result), return; end;
   
    %Extract data from result
    chanInput = tepAll{1,result{1,1}};
    
    if strcmp(chanInput,'All')
        elec = [];
        tepType = 'data';
    elseif ~strncmp(chanInput,'ROI',3) && ~strncmp(chanInput,'GMF',3) && ~strcmp(chanInput,'All')
        elec = chanInput;
        tepType = 'data';
    elseif strncmp(chanInput,'ROI',3)
        tepFor = strtrim(strsplit(chanInput,' '));
        tepType = 'ROI';
        tepName = tepFor{1,2};
    elseif strncmp(chanInput,'GMF',3)
        tepFor = strtrim(strsplit(chanInput,' '));
        tepType = 'GMFA';
        tepName = tepFor{1,2};
    end
    
    xlim = str2num(result{1,2});
    
    if strcmp(result{1,3},'')
        ylim = [];
    else
        ylim = str2num(result{1,3});
    end
    
    if result{1,4} == 0
        CI = 'off';
    elseif result{1,4} == 1
        CI = 'on';
    end   
    
    if result{1,5} == 0
        plotPeak = 'off';
    elseif result{1,5} == 1;
        plotPeak = 'on';
    end
   
end

%Run script from input
if nargin > 2
    tesa_plot(EEG,varargin{:});
    com = sprintf('pop_tesa_plot( %s, %s );', inputname(1), vararg2str(varargin) );
elseif nargin < 2
    if strcmp(tepType,'data') && isempty(elec)
        tesa_plot(EEG,'tepType',tepType,'xlim',xlim,'ylim',ylim,'CI',CI,'plotPeak',plotPeak);
        com = sprintf('pop_tesa_plot( %s, ''tepType'', ''%s'', ''xlim'', %s, ''ylim'', %s, ''CI'',''%s'',''plotPeak'',''%s'' );', inputname(1), tepType, mat2str(xlim), mat2str(ylim), CI, plotPeak );
    elseif strcmp(tepType,'data') && ~isempty(elec)
        tesa_plot(EEG,'tepType',tepType,'elec',elec,'xlim',xlim,'ylim',ylim,'CI',CI,'plotPeak',plotPeak);
        com = sprintf('pop_tesa_plot( %s, ''tepType'', ''%s'', ''elec'', ''%s'', ''xlim'', %s, ''ylim'', %s, ''CI'',''%s'',''plotPeak'',''%s'' );', inputname(1), tepType, elec, mat2str(xlim), mat2str(ylim), CI, plotPeak );
    elseif strcmp(tepType,'ROI') || strcmp(tepType,'GMFA')   
        tesa_plot(EEG,'tepType',tepType,'tepName',tepName,'xlim',xlim,'ylim',ylim,'CI',CI,'plotPeak',plotPeak);
        com = sprintf('pop_tesa_plot( %s, ''tepType'', ''%s'', ''tepName'', ''%s'', ''xlim'', %s, ''ylim'', %s, ''CI'',''%s'',''plotPeak'',''%s'' );', inputname(1), tepType, tepName, mat2str(xlim), mat2str(ylim), CI, plotPeak ); 
    end
end
    

end