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pop_stdplotpac.m
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pop_stdplotpac.m
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% pop_stdpacplot() - Call GUI to compute cross-frequency-coupling coupling.
% Second level function to compute CFC by calling eeg_pac.m
% Usage:
% >> STUDY = pop_stdplotpac(STUDY, ALLEEG);
% Inputs:
% ALLEEG - Top-level EEGLAB vector of loaded EEG structures for the dataset(s)
% in the STUDY. ALLEEG for a STUDY set is typically loaded using
% pop_loadstudy(), or in creating a new STUDY, using pop_createstudy().
% STUDY - EEGLAB STUDY set comprising some or all of the EEG
% datasets in ALLEEG.
%
% Outputs:
% STUDY - The input STUDY set structure modified according to specified user edits,
% if any. Plotted channel measure means (maps, ERSPs, etc.) are added to
% the STUDY structure after they are first plotted to allow quick replotting.
% com - Command executed (on development)
%
% See also:
%
% Author: Ramon Martinez-Cancino, SCCN, 2019
%
% Copyright (C) 2019 Ramon Martinez-Cancino,INC, SCCN
%
% 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 [STUDY, com] = pop_stdplotpac(varargin)
com = []; STUDY = [];
icadefs;
if nargin < 2
help pop_stdplotpac;
return;
end
%Fixed vals for both entries
AllMethod_listgui = {'Mean vector length modulation index (Canolty et al., 2006)',...
'Kullback-Leibler modulation index (Tort et al., 2010)',...
'General linear model (Penny et al., 2008)',...
'Phase Locking Value (Lachaux et al., 1999)',...
'Instantaneous MIPAC (Martinez-Cancino et al., 2019)',...
'Event related MIPAC (Martinez-Cancino et al., 2019)'};
AllMethods = {'mvlmi','klmi','glm','plv','instmipac', 'ermipac'};
alldatatypes = {'Channels', 'ICs Clusters'};
alldatatypes_list = {'channels', 'clusters'};
if ~ischar(varargin{1})
STUDY = varargin{1};
ALLEEG = varargin{2};
% Check for fields here eegpac and pacplotopt
if length(STUDY)>1
error('pop_stdplotpac(): Invalid STUDY input');
end
if ~isfield(STUDY.etc, 'eegpac') || isempty(STUDY.etc.eegpac) || ~isfield(STUDY.etc, 'pacplotopt')
error('pop_stdplotpac(): PAC has not been computed for this dataset');
end
datatype = STUDY.etc.eegpac.datatype; % get data type
% Callbacks
cb_comod_opt = 'pop_stdplotpac(''comod_opt'', gcf);';
cb_comodt_opt = 'pop_stdplotpac(''comodt_opt'', gcf);';
cb_tfpac_opt = 'pop_stdplotpac(''tfpac_opt'', gcf);';
cb_trialpac_opt = 'pop_stdplotpac(''trialbasedpac_opt'', gcf);';
cb_comodplot_clust = 'pop_stdplotpac(''comodclust'', gcf);';
cb_comodplot_comp = 'pop_stdplotpac(''comodcomp'', gcf);';
cb_comodtplot_clust = 'pop_stdplotpac(''comodtclust'', gcf);';
cb_comodtplot_comp = 'pop_stdplotpac(''comodtcomp'', gcf);';
cb_tfplot_clust = 'pop_stdplotpac(''tfpacclust'', gcf);';
cb_tfplot_comp = 'pop_stdplotpac(''tfpaccomp'', gcf);';
cb_trialplot_clust = 'pop_stdplotpac(''trialpacclust'', gcf);';
cb_trialplot_comp = 'pop_stdplotpac(''trialpaccomp'', gcf);';
cb_show_clust = 'pop_stdplotpac(''showclust'', gcf);';
cb_show_comps = 'pop_stdplotpac(''showcomplist'', gcf);';
cb_stat_opt = 'pop_stdplotpac(''stat_opt'',gcf);';
% Gui below
guimethodlist = AllMethod_listgui(find(ismember(AllMethods,STUDY.etc.eegpac.method)));
ph_freqrange = ['[' num2str(minmax(STUDY.etc.eegpac.params.freqs_phase)) ']'];
amp_freqrange = ['[' num2str(minmax(STUDY.etc.eegpac.params.freqs_amp)) ']'];
ph_nfreqs = num2str(numel(STUDY.etc.eegpac.params.freqs_phase));
amp_nfreqs = num2str(numel(STUDY.etc.eegpac.params.freqs_amp));
comod_enable = 'on';
comodt_enable = 'on';
freqtime_enable = 'on';
trialpac_enable = 'on';
% userdata below
% --------------
fig_arg{1}{1} = STUDY;
fig_arg{1}{2} = ALLEEG;
if datatype==1
labellist1 = 'Select channel to plot';
labellist2 = 'Select subject to plot';
else
labellist1 = 'Select cluster to plot';
labellist2 = 'Select component to plot ';
end
uilist = { ...
{'style' 'text' 'string' 'Data type: ' 'FontWeight' 'Bold' } {'style' 'text' 'string' alldatatypes{datatype}} ...
{'style' 'text' 'string' 'PAC Method: ' 'FontWeight' 'Bold' } {'style' 'text' 'string' guimethodlist} ...
{'style' 'text' 'string' 'Freq range [lo hi] (Hz)' 'FontWeight' 'bold' } {'style' 'text' 'string' '# Frequencies' 'fontweight' 'bold'}...
{'style' 'text' 'string' 'Phase data' 'FontWeight' 'Bold' } {'style' 'text' 'string' ph_freqrange} {'style' 'text' 'string' ph_nfreqs} ...
{'style' 'text' 'string' 'Amplitude data ' 'FontWeight' 'Bold' } {'style' 'text' 'string' amp_freqrange} {'style' 'text' 'string' amp_nfreqs} ...
{'style' 'text' 'string' 'Select design:' 'FontWeight' 'Bold' 'HorizontalAlignment' 'center'} {'style' 'popupmenu' 'string' { STUDY.design.name } 'FontWeight' 'Bold' 'tag' 'design' 'value' STUDY.currentdesign } ...
{'style' 'text' 'string' labellist1 'FontWeight' 'Bold' } {} {'style' 'text' 'string' labellist2 'FontWeight' 'Bold'} ...
{'style' 'listbox' 'string' '' 'value' 1 'tag' 'clust_list' 'Callback' cb_show_comps } {'style' 'pushbutton' 'enable' 'on' 'string' 'STATS' 'Callback' cb_stat_opt } {'style' 'listbox' 'string' '' 'tag' 'comp_list' 'max' 2 'min' 1} ...
{'style' 'pushbutton' 'enable' comod_enable 'string' 'Comodulogram (freqs x freqs)' 'Callback' cb_comodplot_clust 'tag' 'plot_comod_clust'} {'style' 'pushbutton' 'enable' comod_enable 'string' 'Params' 'Callback' cb_comod_opt 'tag' 'comod_opt'} {'style' 'pushbutton' 'enable' comod_enable 'string' 'Comodulogram (freqs x freqs)' 'Callback' cb_comodplot_comp 'tag' 'plot_comod_comp'} ...
{'style' 'pushbutton' 'enable' comodt_enable 'string' 'Time-comodulogram (times x freqs x freqs)' 'Callback' cb_comodtplot_clust 'tag' 'plot_comodt_clust'} {'style' 'pushbutton' 'enable' comodt_enable 'string' 'Params' 'Callback' cb_comodt_opt 'tag' 'comodt_opt'} {'style' 'pushbutton' 'enable' comodt_enable 'string' 'Time-comodulogram (times x freqs x freqs)' 'Callback' cb_comodtplot_comp 'tag' 'plot_comodt_comp'} ...
{'style' 'pushbutton' 'enable' freqtime_enable 'string' 'Time-frequency PAC (freqs x times)' 'Callback' cb_tfplot_clust 'tag' 'plot_tf_clust'} {'style' 'pushbutton' 'enable' freqtime_enable 'string' 'Params' 'Callback' cb_tfpac_opt 'tag' 'tfpac_opt'} {'style' 'pushbutton' 'enable' freqtime_enable 'string' 'Time-frequency PAC (freqs x times)' 'Callback' cb_tfplot_comp 'tag' 'plot_tf_comp'} ...
{'style' 'pushbutton' 'enable' trialpac_enable 'string' 'Trial-based PAC (Trials x times)' 'Callback' cb_trialplot_clust 'tag' 'plot_trialpac_clust'} {'style' 'pushbutton' 'enable' trialpac_enable 'string' 'Params' 'Callback' cb_trialpac_opt 'tag' 'trialpac_opt'} {'style' 'pushbutton' 'enable' trialpac_enable 'string' 'Trial-based PAC (Trials x times)' 'Callback' cb_trialplot_comp 'tag' 'plot_trialpac_comp'}...
{}};
guiheight = 14;
guiwidth = 2.05;
%%
geometry = {{guiwidth guiheight [0 0] [1 1]} {guiwidth guiheight [0.4 0] [1 1]}...
{guiwidth guiheight [0 1] [1 1]} {guiwidth guiheight [0.4 1] [1 1]}...
{guiwidth guiheight [0.6 2] [1 1]} {guiwidth guiheight [1.4 2] [1 1]}...
{guiwidth guiheight [0 3] [1 1]} {guiwidth guiheight [0.62 3] [1 1]} {guiwidth guiheight [1.5 3] [1 1]}...
{guiwidth guiheight [0 4] [1 1]} {guiwidth guiheight [0.62 4] [1 1]} {guiwidth guiheight [1.5 4] [1 1]}...
{guiwidth guiheight [0 5] [1 1]} {guiwidth guiheight [0.4 5] [1.65 1]}...
{guiwidth guiheight [0 6] [0.9 1]} {guiwidth guiheight [0.4 6] [1 1]} {guiwidth guiheight [1.15 6] [0.9 1]}...
{guiwidth guiheight [0 7] [0.9 3]} {guiwidth guiheight [0.9 7] [0.25 3]} {guiwidth guiheight [1.15 7] [0.9 3]}...
{guiwidth guiheight [0 10] [0.9 1]} {guiwidth guiheight [0.9 10] [0.25 1]} {guiwidth guiheight [1.15 10] [0.9 1]}...
{guiwidth guiheight [0 11] [0.9 1]} {guiwidth guiheight [0.9 11] [0.25 1]} {guiwidth guiheight [1.15 11] [0.9 1]}...
{guiwidth guiheight [0 12] [0.9 1]} {guiwidth guiheight [0.9 12] [0.25 1]} {guiwidth guiheight [1.15 12] [0.9 1]}...
{guiwidth guiheight [0 13] [0.9 1]} {guiwidth guiheight [0.9 13] [0.25 1]} {guiwidth guiheight [1.15 13] [0.9 1]}...
{guiwidth guiheight [0 13] [0.9 1]} };
[out_param userdat tmp res] = inputgui( 'geom' , geometry, 'uilist', uilist,'helpcom', 'pophelp(''pop_stdplotpac'')',...
'title', 'Plot PAC for STUDY -- pop_stdplotpac()' , 'userdata', fig_arg, 'eval', cb_show_clust);
if ~isempty(userdat)
STUDY = userdat{1}{1};
end
else
hdl = varargin{2}; %figure handle
userdat = get(varargin{2}, 'userdat');
STUDY = userdat{1}{1};
ALLEEG = userdat{1}{2};
datatype = STUDY.etc.eegpac.datatype;
% Check cluster/channels selected
ListBoxClustersObj = findobj(hdl,'tag', 'clust_list');
ListBoxClustersObjVal = get(ListBoxClustersObj,'value');
SelectedClustName = STUDY.etc.eegpac.labels{ListBoxClustersObjVal};
ListBoxCompObj = findobj(hdl,'tag', 'comp_list');
ListBoxCompObjVal = get(ListBoxCompObj,'value');
% Components or subjects
if datatype==1
if ListBoxCompObjVal(1) ~= 1
% channels
subject = STUDY.design(STUDY.currentdesign).cases.value{ListBoxCompObjVal-1};
end
else
clsindx = find(~cellfun('isempty',strfind({STUDY.cluster.name},STUDY.etc.eegpac.labels{ListBoxClustersObjVal})));
subcomplist = {STUDY.datasetinfo(STUDY.cluster(clsindx).sets(1,:)).subject};
allcomplist = STUDY.cluster(clsindx).comps;
end
% if datatype == 1
% SelectedCompName = STUDY.etc.eegpac.labels{ListBoxClustersObjVal};
% else
% SelectedCompName = [];
% end
SelectedCompName = STUDY.etc.eegpac.labels{ListBoxClustersObjVal};
design = get(findobj('parent', hdl, 'tag', 'design') , 'value');
try
switch varargin{1}
case {'comodclust', 'comodtclust', 'tfpacclust','trialpacclust'}
plotting_option = varargin{1};
plotting_option = [ 'plot' plotting_option(1:end-5)];
if datatype == 1
a = ['STUDY = std_' plotting_option '(STUDY,ALLEEG,''' alldatatypes_list{datatype} ''',{' vararg2str(SelectedClustName) '}, ''design'', ' int2str(design) ');' ];
else
a = ['STUDY = std_' plotting_option '(STUDY,ALLEEG,''' alldatatypes_list{datatype} ''',' num2str(clsindx) ', ''design'', ' int2str(design) ');' ];
end
eval(a);
%STUDY.tmphist = sprintf('%s\n%s', STUDY.tmphist, a);
% Update Study history
userdat{1}{1} = STUDY;
set(hdl, 'userdat',userdat);
case {'comodcomp', 'comodtcomp', 'tfpaccomp','trialpaccomp'}
plotting_option = varargin{1};
plotting_option = [ 'plot' plotting_option(1:end-4)];
if ListBoxCompObjVal(1) ~= 1 % check that not all onechan in channel are requested
if datatype == 1
a = ['STUDY = std_' plotting_option '(STUDY,ALLEEG,''' alldatatypes_list{datatype} ''',{' vararg2str({SelectedCompName}) '}, ''subject'', ''' subject ''', ''design'', ' int2str(design) ' );' ];
else
a = ['STUDY = std_' plotting_option '(STUDY,ALLEEG,''' alldatatypes_list{datatype} ''',' num2str(clsindx) ',''comps'',' num2str(ListBoxCompObjVal-1) ', ''design'', ' int2str(design) ' );' ];
end
eval(a);
%STUDY.tmphist = sprintf('%s\n%s', STUDY.tmphist, a);
else
if datatype == 1
a = ['STUDY = std_' plotting_option '(STUDY,ALLEEG,''' alldatatypes_list{datatype} ''',{' vararg2str({SelectedCompName}) '}, ''plotsubjects'', ''on'', ''design'', ' int2str(design) ' );' ];
else
a = ['STUDY = std_' plotting_option '(STUDY,ALLEEG,''' alldatatypes_list{datatype} ''',' num2str(clsindx) ', ''plotsubjects'', ''on'', ''design'', ' int2str(design) ' );' ];
end
eval(a);
%STUDY.tmphist = sprintf('%s\n%s', STUDY.tmphist, a);
end
% Update Study history
userdat{1}{1} = STUDY;
set(hdl, 'userdat',userdat);
case 'comod_opt'
STUDY = pop_comodpacparams(STUDY);
userdat{1}{1} = STUDY;
set(hdl, 'userdat',userdat);
case 'comodt_opt'
STUDY = pop_comodtpacparams(STUDY);
userdat{1}{1} = STUDY;
set(hdl, 'userdat',userdat);
case 'tfpac_opt'
STUDY = pop_tfpacparams(STUDY);
userdat{1}{1} = STUDY;
set(hdl, 'userdat',userdat);
case 'trialbasedpac_opt'
STUDY = pop_trialspacparams(STUDY);
userdat{1}{1} = STUDY;
set(hdl, 'userdat',userdat);
case 'enablebuttons'
switch STUDY.etc.eegpac.pactype
case 'PAC'
set(findobj(hdl,'tag', 'plot_comod_clust'), 'enable', 'on'); set(findobj(hdl,'tag', 'comod_opt'), 'enable', 'on'); set(findobj(hdl,'tag', 'plot_comod_comp'), 'enable', 'on');
set(findobj(hdl,'tag', 'plot_comodt_clust'), 'enable', 'on'); set(findobj(hdl,'tag', 'comodt_opt'), 'enable', 'on'); set(findobj(hdl,'tag', 'plot_comodt_comp'), 'enable', 'on');
set(findobj(hdl,'tag', 'plot_tf_clust'), 'enable', 'on'); set(findobj(hdl,'tag', 'tfpac_opt'), 'enable', 'on'); set(findobj(hdl,'tag', 'plot_tf_clust_comp'), 'enable', 'on');
set(findobj(hdl,'tag', 'plot_trialpac_clust'), 'enable', 'off'); set(findobj(hdl,'tag', 'trialpac_opt'), 'enable', 'off'); set(findobj(hdl,'tag', 'plot_trialpac_comp'), 'enable', 'off');
case 'MIPAC'
set(findobj(hdl,'tag', 'plot_comod_clust'), 'enable', 'on'); set(findobj(hdl,'tag', 'comod_opt'), 'enable', 'on'); set(findobj(hdl,'tag', 'plot_comod_comp'), 'enable', 'on');
set(findobj(hdl,'tag', 'plot_comodt_clust'), 'enable', 'on'); set(findobj(hdl,'tag', 'comodt_opt'), 'enable', 'on'); set(findobj(hdl,'tag', 'plot_comodt_comp'), 'enable', 'on');
set(findobj(hdl,'tag', 'plot_tf_clust'), 'enable', 'on'); set(findobj(hdl,'tag', 'tfpac_opt'), 'enable', 'on'); set(findobj(hdl,'tag', 'plot_tf_clust_comp'), 'enable', 'on');
set(findobj(hdl,'tag', 'plot_trialpac_clust'), 'enable', 'on'); set(findobj(hdl,'tag', 'trialpac_opt'), 'enable', 'off'); set(findobj(hdl,'tag', 'plot_trialpac_comp'), 'enable', 'on');
end
case 'showclust'
if datatype == 1
for i =1: length(STUDY.etc.eegpac.labels)
displayclust{i} = ['All ' STUDY.etc.eegpac.labels{i}];
end
set(findobj(hdl,'tag', 'clust_list'),'String',displayclust, 'Value', 1);
else
for i =1: length(STUDY.etc.eegpac.labels)
clsindx = find(~cellfun('isempty',strfind({STUDY.cluster.name},STUDY.etc.eegpac.labels{i})))
displayclust{i} = [STUDY.etc.eegpac.labels{i} ' (' num2str(length(STUDY.cluster(clsindx).comps)) ' ICs)' ];
end
set(findobj(hdl,'tag', 'clust_list'),'String',displayclust, 'Value', 1);
end
pop_stdplotpac('showcomplist', hdl); % Show componenets/subjects in list
pop_stdplotpac('enablebuttons', hdl); % Enable/disable buttons based on metric
case 'showcomplist'
if datatype == 1
allsubjects = STUDY.design(STUDY.currentdesign).cases.value;
complist = {'All subjects'};
for l = 1:length(allsubjects)
complist{end+1} = [ allsubjects{l} ' ' SelectedClustName ];
end
else
clsindx = find(~cellfun('isempty',strfind({STUDY.cluster.name},STUDY.etc.eegpac.labels{ListBoxClustersObjVal})));
subcomplist = {STUDY.datasetinfo(STUDY.cluster(clsindx).sets(1,:)).subject};
allcomplist = STUDY.cluster(clsindx).comps;
complist = {'All components'};
for l = 1:length(allcomplist)
complist{end+1} = [ subcomplist{l} ' IC' num2str(allcomplist(l)) ];
end
end
set(findobj(hdl,'tag', 'comp_list'),'String',complist, 'Value', 1);
case 'stat_opt' % save the list of selected channels
[STUDY com] = pop_statparams(STUDY);
userdat{1}{1} = STUDY;
set(hdl, 'userdat',userdat); %update information (STUDY)
end
catch
eeglab_error;
end
end