SLURM job scheduling, and added some color repos

Author: fahrenfort

eeg_mvpa/adam_compute_group_ERP.m

@@ -174,7 +174,7 @@
 if isempty(plot_order)
     dirz = dir(folder_name);
     dirz = {dirz([dirz(:).isdir]).name};
-    plot_order = dirz(cellfun(@isempty,strfind(dirz,'.')));
+    plot_order = dirz(~(strcmp(dirz,'.')|strcmp(dirz,'..')));
     if ndirs == 1
         [folder_name, plot_order] = fileparts(folder_name);
         plot_order = {plot_order};
@@ -187,7 +187,7 @@
 else
     dirz = dir(folder_name);
     dirz = {dirz([dirz(:).isdir]).name};
-    dirz = dirz(cellfun(@isempty,strfind(dirz,'.')));
+    dirz = dirz(~(strcmp(dirz,'.')|strcmp(dirz,'..')));
     for cPlot = 1:numel(plot_order)
         dirindex = find(strcmpi(plot_order{cPlot},dirz));
         if isempty(dirindex) % if an exact match cannot be made, look only for the pattern in the first sequency of characters
@@ -258,7 +258,8 @@
 % get filenames
 plotFreq = ''; % this is empty for now, but might be used to look at the ERPs obtained from a TF analysis
 subjectfiles = dir([folder_name filesep channelpool plotFreq filesep '*.mat']);
-[~, condname] = fileparts(folder_name);
+[~, condname,ext] = fileparts(folder_name);
+condname = [condname ext];
 subjectfiles = { subjectfiles(:).name };
 subjectfiles(strncmp(subjectfiles,'.',1)) = []; % remove hidden files
 

eeg_mvpa/adam_compute_group_MVPA.m

@@ -202,7 +202,7 @@
 if isempty(plot_order)
     dirz = dir(folder_name);
     dirz = {dirz([dirz(:).isdir]).name};
-    plot_order = dirz(cellfun(@isempty,strfind(dirz,'.')));
+    plot_order = dirz(~(strcmp(dirz,'.')|strcmp(dirz,'..')));
     if ndirs == 1
         [folder_name, plot_order] = fileparts(folder_name);
         plot_order = {plot_order};
@@ -215,7 +215,7 @@
 else
     dirz = dir(folder_name);
     dirz = {dirz([dirz(:).isdir]).name};
-    dirz = dirz(cellfun(@isempty,strfind(dirz,'.')));
+    dirz = dirz(~(strcmp(dirz,'.')|strcmp(dirz,'..')));
     for cPlot = 1:numel(plot_order)
         dirindex = find(strcmpi(plot_order{cPlot},dirz)); 
         if isempty(dirindex) % if an exact match cannot be made, look only for the pattern in the first sequency of characters
@@ -234,8 +234,28 @@
     end
 end
 
+% when plotting individual subjects in a single plot also need to create a figure and set colors
+if plotsubjects && singleplot
+    fh = figure('name','individual subjects');
+    set(fh, 'Position', get(0,'Screensize'));
+    set(fh,'color','w');
+    % set line colors
+    if ~exist('line_colors','var')
+        line_colors = {[.5 0 0] [0 .5 0] [0 0 .5] [.5 .5 0] [0 .5 .5] [.5 0 .5] [.75 0 0] [0 .75 0] [0 0 .75] [.75 .75 0] [0 .75 .75] [.75 0 .75] };
+    end
+    if ~iscell(line_colors)
+        for c=1:size(line_colors,1)
+            cell_colors{c} = line_colors(c,:);
+        end
+        line_colors = cell_colors;
+    end
+end
+
 % loop through directories (results folders)
 for cdirz = 1:numel(plot_order)
+    if plotsubjects && singleplot
+        cfg.line_color = line_colors{cdirz};
+    end
     [stats(cdirz), cfg] = subcompute_group_MVPA(cfg, [folder_name filesep plot_order{cdirz}], mask);
 end
 
@@ -326,7 +346,8 @@
 
 % get filenames
 subjectfiles = dir([folder_name filesep channelpool plotFreq{1} filesep '*.mat']);
-[~, condname] = fileparts(folder_name);
+[~, condname, ext] = fileparts(folder_name);
+condname = [condname ext];
 subjectfiles = { subjectfiles(:).name };
 subjectfiles(strncmp(subjectfiles,'.',1)) = []; % remove hidden files
 
@@ -342,7 +363,7 @@
 end
 
 % prepare figure in case individual subjects are plotted
-if plotsubjects;
+if plotsubjects && ~singleplot
     fh = figure('name',['individual subjects: ' condname]);
     set(fh, 'Position', get(0,'Screensize'));
     set(fh,'color','w');
@@ -630,6 +651,9 @@
 
     % plot individual subjects
     if plotsubjects
+        if singleplot
+            hold on; % for plotting multiple lines
+        end
         subplot(numSubplots(nSubj,1),numSubplots(nSubj,2),cSubj);
         onestat.ClassOverTime = ClassOverTime;
         onestat.StdError = [];
@@ -644,6 +668,9 @@
         onestat.channelpool = channelpool;
         onestat.cfg = [];
         tmpcfg = cfg;
+        if singleplot
+            tmpcfg.line_colors = {line_color}; % for plotting multiple lines
+        end
         tmpcfg.plot_model = plot_model;
         tmpcfg.plotsubjects = true;
         tmpcfg.plotsigline_method = 'both';

eeg_mvpa/adam_plot_MVPA.m

@@ -69,10 +69,11 @@
 %                               will plot testing on y and training x.
 %   cfg.inverty               = [] (default, for ERP plots default is true); you can choose to plot
 %                               the voltage on the y-axis of ERP plots downward by setting to false.
-%   cfg.plotsigline_method    = 'both' (default); or 'straight'; a straight horizontal line at the 
-%                               bottom of the plot for (clusters of) significant time points in line
-%                               plots is always drawn, but the default option 'both' will also make
-%                               the line of the line plot thicker on these time points. 
+%   cfg.plotsigline_method    = 'both' (default); Alternatively specify 'straight' a straight
+%                               horizontal line at the bottom of the plot for (clusters of)
+%                               significant time points. 'follow' will make the significant lines
+%                               thicker in the graph itself. The default option 'both' will also
+%                               make the line of the line plot thicker on these time points.
 %   cfg.plot_model            = 'BDM' (default); or 'FEM' if stats contains classification results
 %                               of a forward encoding model.
 %
@@ -191,6 +192,12 @@
 end
 
 % set line colors
+if ~iscell(line_colors)
+    for c=1:size(line_colors,1)
+        cell_colors{c} = line_colors(c,:);
+    end
+    line_colors = cell_colors;
+end
 if numel(line_colors)<numel(stats) || isempty(line_colors)
     if numel(stats) > 1
         line_colors = {[.5 0 0] [0 .5 0] [0 0 .5] [.5 .5 0] [0 .5 .5] [.5 0 .5] [.75 0 0] [0 .75 0] [0 0 .75] [.75 .75 0] [0 .75 .75] [.75 0 .75] };
@@ -597,7 +604,7 @@
     % plot significant time points
     if ~isempty(pVals)
         sigdata = data;
-        if strcmpi(plotsigline_method,'straight') || strcmpi(plotsigline_method,'both') && ~isempty(pVals) && ~strcmpi(mpcompcor_method,'none')
+        if strcmpi(plotsigline_method,'straight') || strcmpi(plotsigline_method,'both') 
             if ~singleplot elevate = 1; else elevate = (nGraph-cGraph)+.5; end
             if inverty
                 sigdata(1:numel(sigdata)) = max(acclim) - (diff(acclim)/80)*elevate;
@@ -612,7 +619,7 @@
             end
         end
         sigdata = data;
-        if ~strcmpi(plotsigline_method,'straight')
+        if strcmpi(plotsigline_method,'follow') || strcmpi(plotsigline_method,'both')
             sigdata(pVals>=indiv_pval) = NaN;
             if isnumeric(line_colors{cGraph})
                 H.mainLine=plot(1:numel(sigdata),sigdata,'Color',line_colors{cGraph},'LineWidth',3); % sigline on graph
@@ -637,6 +644,15 @@
                 set(h_legend,'FontSize',12);
             end
         end
+    else
+        if strcmpi(plotsigline_method,'follow') || strcmpi(plotsigline_method,'both')
+            sigdata = data;
+            if isnumeric(line_colors{cGraph})
+                H.mainLine=plot(1:numel(sigdata),sigdata,'Color',line_colors{cGraph},'LineWidth',3); % sigline on graph
+            else
+                H.mainLine=plot(1:numel(sigdata),sigdata,line_colors{cGraph},'LineWidth',3); % sigline on graph
+            end
+        end
     end
     if unique(numel(acclim)) == 2
         ylim(acclim);

general_stats/Corr_toolbox_v2/Anscombe.mat

@@ -0,0 +1,11 @@
+   1.0000000e+01   8.0400000e+00   1.0000000e+01   9.1400000e+00   1.0000000e+01   7.4600000e+00   8.0000000e+00   6.5800000e+00
+   8.0000000e+00   6.9500000e+00   8.0000000e+00   8.1400000e+00   8.0000000e+00   6.7700000e+00   8.0000000e+00   5.7600000e+00
+   1.3000000e+01   7.5800000e+00   1.3000000e+01   8.7400000e+00   1.3000000e+01   1.2740000e+01   8.0000000e+00   7.7100000e+00
+   9.0000000e+00   8.8100000e+00   9.0000000e+00   8.7700000e+00   9.0000000e+00   7.1100000e+00   8.0000000e+00   8.8400000e+00
+   1.1000000e+01   8.3300000e+00   1.1000000e+01   9.2600000e+00   1.1000000e+01   7.8100000e+00   8.0000000e+00   8.4700000e+00
+   1.4000000e+01   9.9600000e+00   1.4000000e+01   8.1000000e+00   1.4000000e+01   8.8400000e+00   8.0000000e+00   7.0400000e+00
+   6.0000000e+00   7.2400000e+00   6.0000000e+00   6.1300000e+00   6.0000000e+00   6.0800000e+00   8.0000000e+00   5.2500000e+00
+   4.0000000e+00   4.2600000e+00   4.0000000e+00   3.1000000e+00   4.0000000e+00   5.3900000e+00   1.9000000e+01   1.2500000e+01
+   1.2000000e+01   1.0840000e+01   1.2000000e+01   9.1300000e+00   1.2000000e+01   8.1500000e+00   8.0000000e+00   5.5600000e+00
+   7.0000000e+00   4.8200000e+00   7.0000000e+00   7.2600000e+00   7.0000000e+00   6.4200000e+00   8.0000000e+00   7.9100000e+00
+   5.0000000e+00   5.6800000e+00   5.0000000e+00   4.7400000e+00   5.0000000e+00   5.7300000e+00   8.0000000e+00   6.8900000e+00