% STUDY - studyset structure containing some or all files in ALLEEG
% measure - Measure to display. One from: {'daterp','datspec','icaerp','icaspec'}
% dataflag - [1|0] Flag for 'data' or 'limoresults' respectively
% level - [1|2] Level of analysis to plot. [1] Single subject
% analysis results. [2] Group level analysis results.
% stats - Cell array of {'property','property_value',...} of stats settings.
% Properties can be: pvalue ('p'), ('MCC, Number of bootstrap
% ('bootstrap'),('tfce'). If not provided, defaults are:
% {'p',0.05,'MCC',1,'dir',pwd,'bootstrap',0,'tfce',0};
% plottype - Type of plot [1|2|3]
% If Plot type 1 ('plottype', 1),
% subjindx - Index on STUDY.datasetinfo.subject of the subject to
% plot.
% testindx - Index (if level 1of the test to plot.
% I.E.
% std_limoresults(STUDY,'flagdata',1,'plottype',1,'measure','daterp','level',1,'subjindx',1,'testindx',1); % To do
% std_limoresults(STUDY,'flagdata',0,'plottype',1,'measure','daterp','level',1,'subjindx',1,'testindx',1);
%
% If Plot type 2 ('plottype', 2)
%
%
% Optional inputs:
% 'measure' - ['daterp'|'icaerp'|'datspec'|'icaspec'|'datersp'|'icaersp']
% Example
% %Plot 1 (imagesc + topo)
% std_limoresults(STUDY,'plottype',1,'flagdata',1,'measure','daterp','level',1,'subjindx',1,'regressor',{'[1]'});% To do (data single subj level)
% % To do (data group level)
% std_limoresults(STUDY,'plottype',1,'flagdata',0,'measure','daterp','level',1,'subjindx',1,'testindx',1); % (results single subj level)
% std_limoresults(STUDY,'plottype',1,'flagdata',0,'measure','daterp','level',2,'testindx',1); % (results group level)
%
% %Plot 2 (topo)
% std_limoresults(STUDY,'plottype',2,'flagdata',1,'measure','daterp','level',1,'subjindx',1,'regressor',{'[1]'});% (data single subj level)
% % To do (data group level)
% std_limoresults(STUDY,'plottype',2,'flagdata',0,'measure','daterp','level',1,'subjindx',1,'testindx',1); % (results single subj level)
% std_limoresults(STUDY,'plottype',2,'flagdata',0,'measure','daterp','level',2,'testindx',1); % (results group level)
%
% % Plot 3 (Time series + significance)
% std_limoresults(STUDY,'plottype',3,'flagdata',1,'measure','daterp','level',1,'subjindx',1,'regressor',{'[1]'},'chanindx',6); % (data single subj level)
% % To do (data group level)
% std_limoresults(STUDY,'plottype',3,'flagdata',0,'measure','daterp','level',1,'subjindx',1,'testindx',1,'regressor',{'[1 2]'},'chanindx',6); % (results single subj level)
% std_limoresults(STUDY,'plottype',3,'flagdata',0,'measure','daterp','level',2,'testindx',1,'chanindx',6);
% Copyright (C) 2016 Ramon Martinez
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:
%
% 1. Redistributions of source code must retain the above copyright notice,
% this list of conditions and the following disclaimer.
%
% 2. Redistributions in binary form must reproduce the above copyright notice,
% this list of conditions and the following disclaimer in the documentation
% and/or other materials provided with the distribution.
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
% THE POSSIBILITY OF SUCH DAMAGE.
function std_limoresults(STUDY,varargin)
if nargin < 1
help std_limoresults;
return;
end
measure_list = {'daterp', 'datspec', 'icaerp', 'icaspec'};
opt = finputcheck(varargin, { 'plottype' 'integer' [1 2 3] [] ;
'flagdata' 'integer' [1,0] '' ;
'measure' 'string' measure_list '' ;
'subjindx' 'integer' [] [] ;
'level' 'integer' [1 2] [] ;
'testindx' 'integer' [] [] ;
'chanindx' 'integer' [] [] ;
'regressor' 'cell' [] {};
'stats' 'cell' { } {}}, 'std_limoresults');
if ischar(opt), error(opt); end
% Stats
for i = 1:2:numel(opt.stats)
handles.(opt.stats{i}) = opt.stats{i+1};
end
try handles.p ; catch, handles.p = 0.05; end
try handles.MCC ; catch, handles.MCC = 1; end
try handles.dir ; catch, handles.dir = pwd; end
try handles.bootstrap ; catch, handles.bootstrap = 0; end
try handles.tfce ; catch, handles.tfce = 0; end
% Limo indx
limostruct_indx = find(~cellfun(@isempty,strfind({STUDY.design(STUDY.currentdesign).limo.datatype},opt.measure)));
if isempty(limostruct_indx)
fprintf(2,['std_limoresults error: Can not find measeure ' opt.measure '\n']);
exit;
end
% --- EEGLAB ADDED ---
% Loading files
if opt.level == 2
files = {STUDY.design(STUDY.currentdesign).limo(limostruct_indx).groupmodel.filename};
[PathName, tmp1, tmp2] = fileparts(files{opt.testindx});
FileName = [tmp1 tmp2]; clear tmp1 tmp2;
elseif opt.level == 1
if opt.flagdata
PathName = fileparts(STUDY.design(STUDY.currentdesign).limo(limostruct_indx).model(opt.subjindx).filename{1});
FileName = '';
else
if opt.plottype == 3, opt.testindx = 1; end
[PathName, tmp1, tmp2] = fileparts(STUDY.design(STUDY.currentdesign).limo(limostruct_indx).model(opt.subjindx).filename{opt.testindx});
FileName = [tmp1 tmp2]; clear tmp1 tmp2;
end
else
fprintf(2,['std_limoresults error: Not a valid input ''' num2str(opt.level) ''' \n']);
return;
end
% ---------------------
switch opt.plottype
% --------------------------------------------------------
% IMAGE ALL (COMBINED PLOT)
% --------------------------------------------------------
case 1
if ~(opt.flagdata)
handles.LIMO = load(fullfile(PathName,'LIMO.mat'));% eeglab mod
% check if bootstrap or tfce should be computed
% ---------------------------------------------
% 1st level
if handles.LIMO.LIMO.Level == 1;
if handles.bootstrap == 1 && ~exist(sprintf('H0%sH0_%s', filesep, FileName), 'file') ...
&& strncmp(FileName,'con',3) == 0 && strncmp(FileName,'ess',3) ==0
if strcmp(questdlg('Level 1: compute all bootstraps?','bootstrap turned on','Yes','No','No'),'Yes');
LIMO = handles.LIMO.LIMO;
LIMO.design.bootstrap = 1;
if handles.tfce == 1
LIMO.design.tfce = 1;
end
save LIMO LIMO
if strcmp(handles.LIMO.LIMO.Analysis,'Time-Frequency')
limo_eeg_tf(4);
else
limo_eeg(4);
end
end
end
if handles.tfce == 1 && ~exist(sprintf('TFCE%stfce_%s', filesep, FileName), 'file') ...
&& exist(sprintf('H0%sH0_%s', filesep, FileName), 'file') && strncmp(FileName,'con',3) == 0 ...
&& strncmp(FileName,'ess',3) ==0
if strcmp(questdlg('Level 1: compute all tfce?','tfce turned on','Yes','No','No'),'Yes');
LIMO = handles.LIMO.LIMO;
LIMO.design.tfce = 1;
save LIMO LIMO
if strcmp(handles.LIMO.LIMO.Analysis,'Time-Frequency')
limo_eeg_tf(4);
else
limo_eeg(4);
end
end
end
end
% contrasts stuff
if handles.bootstrap == 1 && ~exist(sprintf('H0%sH0_%s', filesep, FileName), 'file')
if strncmp(FileName,'con',3)
load Yr; cd H0; H0_Betas.mat;
result = limo_contrast(Yr, H0_Betas, handles.LIMO.LIMO, 0,3); clear Yr H0_Betas
elseif strncmp(FileName,'ess',3)
load Yr; cd H0; H0_Betas.mat;
result = limo_contrast(Yr, H0_Betas, handles.LIMO.LIMO, 1,3); clear Yr H0_Betas
end
end
if handles.tfce == 1 && ~exist(sprintf('TFCE%stfce_%s', filesep, FileName), 'file') ...
&& exist(sprintf('H0%sH0_%s', filesep, FileName), 'file')
if strncmp(FileName,'con',3)
load(FileName);
if strcmp(handles.LIMO.LIMO.Analysis,'Time-Frequency'); x = 3;
else [x,y,z] = size(con); if x~=1; x=2; end
end
tfce_score = limo_tfce(x,squeeze(con(:,:,2)),handles.LIMO.LIMO.data.neighbouring_matrix);
cd TFCE;
filename2 = sprintf('tfce_%s', FileName);
save(filename2, 'tfce_score');
clear con tfce_score
cd('..')
cd('H0')
filename = sprintf('H0_%s', FileName);
load(filename);
tfce_H0_score = limo_tfce(x,squeeze(H0_ess(:,:,2,:)),handles.LIMO.LIMO.data.neighbouring_matrix);
filename2 = sprintf('tfce_%s',filename); save ([filename2], 'tfce_H0_score'); clear H0_con tfce_score
elseif strncmp(FileName,'ess',3)
load(FileName);
if strcmp(handles.LIMO.LIMO.Analysis,'Time-Frequency'); x = 3;
else [x,y,z] = size(ess); if x~=1; x=2; end
end
tfce_score = limo_tfce(x,squeeze(ess(:,:,2)),handles.LIMO.LIMO.data.neighbouring_matrix);
cd TFCE; filename2 = sprintf('tfce_%s',FileName); save ([filename2], 'tfce_score'); clear ess tfce_score
cd('..'); cd H0; filename = sprintf('H0_%s',FileName); load(filename);
tfce_H0_score = limo_tfce(x,squeeze(H0_ess(:,:,2,:)),handles.LIMO.LIMO.data.neighbouring_matrix);
filename2 = sprintf('tfce_%s',filename); save ([filename2], 'tfce_H0_score'); clear H0_ess tfce_score
end
end
% 2nd level
nboot = 1000;
if handles.LIMO.LIMO.Level == 2
if handles.bootstrap == 1 && ~exist(sprintf('H0%sH0_%s', filesep, FileName), 'file')
if strncmp(FileName,'one_sample',10)
load Yr; limo_random_robust(1,Yr,eval(FileName(28:end-4)),nboot,handles.tfce); clear Yr;
LIMO.design.bootstrap = 1; save LIMO LIMO
elseif strncmp(FileName,'two_samples',11)
load Y1r; load Y2r; limo_random_robust(2,Y1r,Y2r,eval(FileName(29:end-4)),nboot,handles.tfce); clear Y1r Y2r;
LIMO.design.bootstrap = 1; save LIMO LIMO
elseif strncmp(FileName,'paired_samples',14)
load Y1r; load Y2r; limo_random_robust(3,Y1r,Y2r,eval(FileName(32:end-4)),nboot,handles.tfce); clear Y1r Y2r;
LIMO.design.bootstrap = 1; save LIMO LIMO
elseif strncmp(FileName,'Repeated_measures',17)
warndlg2('repeated measure ANOVA bootstrap is not available at this stage, please use the random effect GUI','action not performed')
else
if strcmp(handles.LIMO.LIMO.Analysis,'Time-Frequency')
limo_eeg_tf(4);
else
limo_eeg(4);
end
end
end
if handles.tfce == 1 && ~exist(sprintf('TFCE%stfce_%s', filesep, FileName), 'file') ...
&& exist(sprintf('H0%sH0_%s', filesep, FileName), 'file')
mkdir tfce; load(FileName); load(sprintf('H0%sH0_%s', filesep, FileName));
if strncmp(FileName,'one_sample',10)
parameter = eval(FileName(28:end-4));
tfce_name = sprintf('tfce_one_sample_ttest_parameter_%g',parameter);
tfce_H0_name = sprintf('tfce_H0_one_sample_ttest_parameter_%g',parameter);
if strcmp(handles.LIMO.LIMO.Analysis,'Time-Frequency');
x = size(one_sample,1);
if x==1
x=2; LIMO.LIMO.data.neighbouring_matrix = [];
else
x=3;
end
tfce_one_sample = limo_tfce(x,squeeze(one_sample(:,:,:,4)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['tfce', filesep, tfce_name], 'tfce_one_sample'); clear tfce_one_sample;
tfce_H0_one_sample = limo_tfce(x,squeeze(H0_one_sample(:,:,:,1,:)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['H0', filesep, tfce_H0_name],'tfce_H0_one_sample'); clear tfce_H0_one_sample;
else
x = size(one_sample,1); if x~=1; x=2; end
tfce_one_sample = limo_tfce(x,squeeze(one_sample(:,:,4)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['tfce', filesep, tfce_name], 'tfce_one_sample'); clear tfce_one_sample;
tfce_H0_one_sample = limo_tfce(x,squeeze(H0_one_sample(:,:,1,:)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['H0', filesep, tfce_H0_name],'tfce_H0_one_sample'); clear tfce_H0_one_sample;
end
elseif strncmp(FileName,'two_samples',11)
parameter = eval(FileName(29:end-4));
tfce_name = sprintf('tfce_two_samples_ttest_parameter_%g',parameter);
tfce_H0_name = sprintf('tfce_H0_two_samples_ttest_parameter_%g',parameter);
if strcmp(handles.LIMO.LIMO.Analysis,'Time-Frequency');
x = size(one_sample,1);
if x==1
x=2; LIMO.LIMO.data.neighbouring_matrix = [];
else
x=3;
end
tfce_two_samples = limo_tfce(x,squeeze(two_samples(:,:,:,4)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['tfce', filesep, tfce_name], 'tfce_two_samples'); clear tfce_two_samples;
tfce_H0_two_samples = limo_tfce(x,squeeze(H0_two_samples(:,:,:,1,:)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['H0', filesep, tfce_H0_name],'tfce_H0_two_samples'); clear tfce_H0_two_samples;
else
x = size(two_samples,1); if x~=1; x=2; end
tfce_two_samples = limo_tfce(x,squeeze(two_samples(:,:,4)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['tfce', filesep, tfce_name], 'tfce_two_samples'); clear tfce_two_samples;
tfce_H0_two_samples = limo_tfce(x,squeeze(H0_two_samples(:,:,1,:)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['H0', filesep, tfce_H0_name],'tfce_H0_two_samples'); clear tfce_H0_two_samples;
end
elseif strncmp(FileName,'paired_samples',14)
parameter = eval(FileName(32:end-4));
tfce_name = sprintf('tfce_paired_samples_ttest_parameter_%g',parameter);
tfce_H0_name = sprintf('tfce_H0_paired_samples_ttest_parameter_%g',parameter);
if strcmp(handles.LIMO.LIMO.Analysis,'Time-Frequency')
x = size(one_sample,1);
if x==1
x=2; LIMO.LIMO.data.neighbouring_matrix = [];
else
x=3;
end
tfce_paired_samples = limo_tfce(x,squeeze(paired_samples(:,:,:,4)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['tfce', filesep, tfce_name], 'tfce_paired_samples'); clear tfce_paired_samples;
tfce_H0_paired_samples = limo_tfce(x,squeeze(H0_paired_samples(:,:,:,1,:)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['H0', filesep, tfce_H0_name],'tfce_H0_paired_samples'); clear tfce_H0_paired_samples;
else
x = size(paired_samples,1); if x~=1; x=2; end
tfce_paired_samples = limo_tfce(x,squeeze(paired_samples(:,:,4)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['tfce', filesep, tfce_name], 'tfce_paired_samples'); clear tfce_paired_samples;
tfce_H0_paired_samples = limo_tfce(x,squeeze(H0_paired_samples(:,:,1,:)),handles.LIMO.LIMO.data.neighbouring_matrix);
save(['H0', filesep, tfce_H0_name],'tfce_H0_paired_samples'); clear tfce_H0_paired_samples;
end
elseif strncmp(FileName,'Repeated_measures',17)
msgbox('repeated measure ANOVA tfce is not available at this stage, please use the random effect GUI','action not performed','warn')
else
if strcmp(handles.LIMO.LIMO.Analysis,'Time-Frequency')
limo_eeg_tf(4);
else
limo_eeg(4);
end
end
end
end
% do the figure
% -------------
limo_display_results(1,FileName,PathName,handles.p,handles.MCC,handles.LIMO.LIMO);
cd(handles.dir);
else
fprintf(2,'std_limoresults error: Under construction \n');
end
% --------------------------------------------------------
% TOPOPLOT (SCALP MAPS)
% --------------------------------------------------------
case 2
handles.LIMO = load(fullfile(PathName,'LIMO.mat'));
if opt.flagdata
limo_display_results(2,'Yr.mat',PathName,handles.p,handles.MCC,handles.LIMO.LIMO,1,'regressor',opt.regressor);
else
limo_display_results(2,FileName,PathName,handles.p,handles.MCC,handles.LIMO.LIMO);
end
cd(handles.dir);
% --------------------------------------------------------
% COURSE PLOT (TIME COURSE)
% --------------------------------------------------------
case 3
% --- EEGLAB ADDED ---
FileName = 'LIMO.mat';
% Getting Channels
selected_chan = opt.chanindx; %get(obj.gui_h.listbox_elect2plot,'Value')-1;
% Getting Regressor
%selected_reg = get(obj.gui_h.popupmenu_modelvar2plot,'Value');
%---------------------
cd(PathName);
try
handles.LIMO = load('LIMO.mat');
if strncmp(handles.LIMO.LIMO.design.name,'one sample',9)
files = dir('*.mat');
for i=1:length(files)
if strncmp(files(i).name,'one_sample',10)
FileName = files(i).name;
end
end
elseif strncmp(handles.LIMO.LIMO.design.name,'two samples',9)
files = dir('*.mat');
for i=1:length(files)
if strncmp(files(i).name,'two_samples',11)
FileName = files(i).name;
end
end
elseif strncmp(handles.LIMO.LIMO.design.name,'paired t-test',12)
files = dir('*.mat');
for i=1:length(files)
if strncmp(files(i).name,'paired_sample',13)
FileName = files(i).name;
end
end
elseif strncmp(handles.LIMO.LIMO.design.name,'Repeated measures ANOVA',22)
if handles.LIMO.LIMO.design.nb_conditions == 1 && length(handles.LIMO.LIMO.design.repeated_measure) == 1
FileName = 'Rep_ANOVA_Factor_1.mat';
else
[FileName,PathName,FilterIndex]=uigetfile('*.mat','Which Effect to plot?');
end
end
catch
LIMO = []; handles.LIMO = LIMO;
end
if opt.flagdata && opt.level ==1
limo_display_results(3,FileName,PathName,handles.p,handles.MCC,handles.LIMO.LIMO,0,'channels', {num2str(selected_chan)}, 'regressor',opt.regressor,'plot3type','Original');
elseif ~(opt.flagdata) && opt.level == 1
plot3type_val = questdlg('Plotting ERP','ERP Options','Modelled','Adjusted','Adjusted');
limo_display_results(3,FileName,PathName,handles.p,handles.MCC,handles.LIMO.LIMO,0,'channels', {num2str(selected_chan)}, 'regressor',opt.regressor,'plot3type',plot3type_val);
elseif opt.level == 2
limo_display_results(3,FileName,PathName,handles.p,handles.MCC,handles.LIMO.LIMO,0,'channels', {num2str(selected_chan)});
end
cd(handles.dir);
% --------------------------------------------------------
% FrequenciesTime/Freq Plane
% --------------------------------------------------------
case 4
fprintf(2,'std_limoresults error: Under construction \n');
end
end
Datasets
Models
