Merge pull request #114 from fahrenfort/bugfixes

FEM updates

eeg_mvpa/adam_plot_BDM_weights.m

@@ -299,11 +299,11 @@
 set(gcf,'color','w');
 title(title_text,'FontSize', 12);
 if strcmp(imgtype,'vec') % chanlocs' +Y
-    topoplot_jjf(plot_data,convertlocs(chanlocs,'cart2topo'),'maplimits',weightlim,'style','blank','electrodes','on','nosedir',nosedir,'emarker',{'.','k',5,1},'emarker2',{elecs,'.','k',15,1}); %
+    topoplot_jjf(plot_data,convertlocs(chanlocs,'cart2topo'),'maplimits',weightlim,'style','blank','electrodes','on','plotrad',.65,'nosedir',nosedir,'emarker',{'.','k',5,1},'emarker2',{elecs,'.','k',15,1}); %
 elseif strcmp(imgtype,'png')
-    topoplot_jjf(plot_data,convertlocs(chanlocs,'cart2topo'),'maplimits',weightlim,'style','map','electrodes','off','shading','interp','nosedir',nosedir,'hcolor','none');
+    topoplot_jjf(plot_data,convertlocs(chanlocs,'cart2topo'),'maplimits',weightlim,'style','map','electrodes','off','plotrad',.65,'shading','interp','nosedir',nosedir,'hcolor','none');
 else
-    topoplot_jjf(plot_data,convertlocs(chanlocs,'cart2topo'),'maplimits',weightlim,'style','map','electrodes','on','nosedir',nosedir,'emarker2',{elecs,'o','k',10,1}); % 'electrodes','ptslabels', 'plotrad',.7
+    topoplot_jjf(plot_data,convertlocs(chanlocs,'cart2topo'),'maplimits',weightlim,'style','map','electrodes','on','plotrad',.65,'nosedir',nosedir,'emarker2',{elecs,'o','k',10,1}); % 'electrodes','ptslabels', 'plotrad',.7
     h = cbar('vert');
     set(get(h,'title'),'string',' ');
     %h = colorbar;

eeg_mvpa/adam_plot_CTF.m

@@ -9,7 +9,6 @@
 %
 % The cfg (configuration) input structure can contain the following:
 %       cfg.plotfield           = 'CTF' or 'CTFpercond';
-%       cfg.plottype            = '2D' or '3D'
 %       cfg.mpcompcor_method    = 'cluster_based';
 %       cfg.tail                = 'both';
 %       cfg.trainlim            = [];
@@ -25,8 +24,10 @@
 %       cfg.reduce_dims         = 'diag', 'avtrain', 'avtest', 'avtraintest', 'avfreq'
 %       cfg.weightlim           = [];
 %       cfg.colorlim            = [];
-%       cfg.CTFtime             = [];  
-%       cfg.BLtime              = [];
+%       cfg.CTFtime             = []; indicates the time window over which the CTF should be
+%                                 averaged. If empty, the CTF is plotted over time.
+%       cfg.BLtime              = []; indicates a baseline window for which the CTF should be
+%                                 plotted
 %       cfg.ytick               = .1;
 %       
 % part of the ADAM toolbox, by J.J.Fahrenfort, VU, 2017/2018
@@ -43,16 +44,24 @@
 plotfield = 'CTF';
 folder = '';
 startdir = '';
-singleplot = false;
+singleplot = true;
+CTFtime = [];
 BLtime = [];
 reduce_dims = [];
-plottype = '3D';
 line_colors = [];
-ytick = .05;
+ytick = .1;
+trainlim = [];
+testlim = [];
 v2struct(cfg);
 
 containsbaseline = ~isempty(BLtime) && cfg.BLtime(1)<= cfg.BLtime(2);
 
+if isempty(CTFtime)
+    plottype = '3D';
+else
+    plottype = '2D';
+end
+
 % set plot type
 if strcmpi(plottype,'3D')
     singleplot = false; % cannot plot 3D plots in single graph
@@ -79,7 +88,7 @@
     end
 end
 nameOfStruct2Update = 'cfg';
-cfg = v2struct(line_colors,singleplot,containsbaseline,ytick,nameOfStruct2Update);
+cfg = v2struct(plottype,line_colors,singleplot,containsbaseline,ytick,trainlim,testlim,nameOfStruct2Update);
 
 v2struct(stats(1).settings,{'fieldNames','dimord'});
 
@@ -156,7 +165,7 @@
     avgctfstruct(cStats).condname = stats(cStats).condname;
 
     % put in legend
-    if ~singleplot || (singleplot && cStats == numel(stats))
+    if (~singleplot || (singleplot && cStats == numel(stats))) && exist('legend_text','var')
         legend(legend_text);
         legend boxoff;
     end
@@ -575,9 +584,9 @@
             H.mainLine=plot3(1:numel(sigline),ones(size(sigline))*addy,sigline,'k','LineWidth',8);
         end
     end
-    if ~all(isnan((sigline)))
-        wraptext('Due to a bug in the way Matlab exports figures (the ''endcaps'' property in OpenGL is set to''on'' by default), the ''significance lines'' near the time line are not correctly plotted when saving as .eps or .pdf. The workaround is to open these plots in Illustrator, manually select these lines and select ''butt cap'' for these lines (under the ''stroke'' property).');
-    end
+%     if ~all(isnan((sigline)))
+%         wraptext('Due to a bug in the way Matlab exports figures (the ''endcaps'' property in OpenGL is set to''on'' by default), the ''significance lines'' near the time line are not correctly plotted when saving as .eps or .pdf. The workaround is to open these plots in Illustrator, manually select these lines and select ''butt cap'' for these lines (under the ''stroke'' property).');
+%     end
 
     % NEW
     % determine time tick

eeg_mvpa/plot_FEM_weights.m → eeg_mvpa/adam_plot_FEM_weights.m

@@ -1,7 +1,8 @@
-function avweightstruct = plot_FEM_weights(stats,cfg)
-% plot FEM weights for a specific time range or frequency range
+function avweightstruct = adam_plot_FEM_weights(cfg,stats)
+% ADAM_PLOT_FEM_WEIGHTS generates topographical maps of classifier forward encoding weights over a
+% specified time interval. Requires as input the output of adam_compute_group_MVPA.
 %
-% J.J.Fahrenfort, VU 2016
+% J.J.Fahrenfort, VU 2016, 2019
 
 % main loop
 for c=1:numel(stats)
@@ -29,7 +30,7 @@
 timelim = 250; % indicate time or period for which to compute weights in ms, if empty plots time with highest average weight
 freqlim = []; % indicate freq or freq range for which to compute weights in ms, if empty plots frequency with heighest average weight
 weightlim = []; % indicate color range to plot
-normalized = false; % can be false (default) or true (z-scoring is performed)
+normalized = true; % can be false (default) or true (z-scoring is performed)
 imgtype = [];
 indiv_pval = .05;
 cluster_pval = .05;
@@ -175,6 +176,10 @@
     end
 end
 
+% colormap
+cmap  = brewermap([],'*RdBu');
+colormap(gcf,cmap);
+
 % return the averages
 avweightstruct.chanlocs = chanlocs;
 avweightstruct.avWeights = avWeights;