major update PB_DRAFT, also: moving sound vPrime

subtools/draft/@pb_draft/draft.m

@@ -7,7 +7,8 @@ function draft(obj)
 
 % PBToolbox (2018): JJH: j.heckman@donders.ru.nl
 
-   %% Create figure
+   %% Initialize Draft
+   %  Make figure, select parents, and set layouts
    
    % 	Select parent/make figure
    if isempty(obj(1).parent)
@@ -19,47 +20,47 @@ function draft(obj)
    %  Set figure settings
    set(obj(1).parent,'color','w');
    t = sgtitle(obj(1).parent,obj(1).title);
-   set(t,'FontSize',20);
+   set(t,'FontSize',18);
    
    ax       = gobjects(0);
    objsz    = size(obj);
    
    %% Super labels
-   %  Check if labels are the same, and prep super labels
+   %  Check and prepare superlabels
    
-   lab_x = true; lab_y = true;
+   %  Check labels
+   bool = true; if numel(obj) == 1; bool = false; end
+   lab_x = bool; lab_y = bool;
    for iObj = 1:numel(obj) 
       if ~strcmp(obj(1).labels.xlab, obj(iObj).labels.xlab); lab_x = false; end
       if ~strcmp(obj(1).labels.ylab, obj(iObj).labels.ylab); lab_y = false; end
    end
+   
+   %  Set superlabels
    obj(1).labels.supx = lab_x;
    obj(1).labels.supy = lab_y;
    
    
-   %%  Set Compare axis
-   cmp      = length(unique(obj(1).pva.axcomp.feature));
-   cmpsz    = [1 1];
-   nObj     = numel(obj)*cmp;
+   %%  Set Compare Axis
+   %  Check and set comparing axis
    
-   if min(objsz)>1 
-      cmp = 1; 
-   else
-      if objsz(1)<objsz(2)
-         % horizontal direction
-         cmpsz(1) = cmp;
-      else
-         % vertical direction
-         cmpsz(2) = cmp;
-      end
-   end
+   nCmp     = length(unique(obj(1).pva.axcomp.feature));
+   if min(objsz) > 1; nCmp = 1; end
    
-      %% Create (sub)plots
+   cmpsz    = [1 1];
+   nObj     = numel(obj) * nCmp;
+
+   [~,cmpInd]     = max(cmpsz);
+   cmpsz(cmpInd)  = nCmp; 
+   cmpsz          = fliplr(cmpsz);
+   
+   %% Create Plots
    %  Draft each subplot
    
    for iObj = 1:numel(obj)
       % Repeat for comparing axis
-      for iCmp = 1:cmp
-         cObj    = (iObj-1)*cmp + iCmp;
+      for iCmp = 1:nCmp
+         cObj    = (iObj-1)*nCmp + iCmp;
          
          %  Make Axes 
          Ax       = pb_invidx([objsz(1)*cmpsz(1), objsz(2)*cmpsz(2)],cObj);   % reverse get axes index
@@ -70,19 +71,15 @@ function draft(obj)
          axis(obj(Ax2Obj).pva.axis);
          hold on;
          
-         % Select data
-         uFeat    = unique(obj(1).pva.axcomp.feature);
-         sel      = obj(1).pva.axcomp.feature == uFeat(iCmp);
+         %  Select data
+         features = unique(obj(1).pva.axcomp.feature);
+         sel      = obj(1).pva.axcomp.feature == features(iCmp);
+         
          D        = obj(Ax2Obj).pva;
          D.x      = D.x(sel);
          D.y      = D.y(sel);
          D.color  = D.color(sel);
          
-         % Set colors
-         nCol = 1;
-         if ~obj(iObj).pva.continious 
-            nCol = length(unique(obj(iObj).pva.color));
-         end
 
          %  Plot all graphs
          for iDP = 1:length(obj(iObj).dplot)
@@ -99,12 +96,11 @@ function draft(obj)
       end
    end
    
-   %% Adjust axis handles
+   %% Adjust Axis Handles
    %  Set super labels
    
    %  TO DO:
-   %  1. Optionalize subplots to have squared/linked/fixed axis
-   %  2. Scale and move axis to make graph nice, pleasing and non-overlapping
+   %  1. Scale and move axis to make graph nice, pleasing and non-overlapping
    obj.make_axes(ax);
    obj.make_suplabel;
 end

subtools/draft/@pb_draft/draft2.m

-function draft(obj)
-% PB_DRAFT>DRAFT
-%
-% OBJ.DRAFT will draw a figure from a pb_draft-object.
-%
-% See also PB_DRAFT, SET_LABELS, SET_TITLE, SET_GRID, PRINT
-
-% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
-
-   %% Create figure
-   
-   % 	Select parent/make figure
-   if isempty(obj(1).parent)
-      for iObj = 1:numel(obj)
-      	obj(iObj).parent = gcf;
-      end
-   end
-   
-   %  Set figure settings
-   set(obj(1).parent,'color','w');
-   t = sgtitle(obj(1).parent,obj(1).title);
-   set(t,'FontSize',20);
-   
-   ax       = gobjects(0);
-   dsz      = size(obj);
-   
-   %% Super labels
-   %  Check if labels are the same, and prep super labels
-   
-   lab_x = true; lab_y = true;
-   for iObj = 1:numel(obj) 
-      if ~strcmp(obj(1).labels.xlab, obj(iObj).labels.xlab); lab_x = false; end
-      if ~strcmp(obj(1).labels.ylab, obj(iObj).labels.ylab); lab_y = false; end
-   end
-   obj(1).labels.supx = lab_x;
-   obj(1).labels.supy = lab_y;
-      
-   %% Create (sub)plots
-   %  Draft each subplot
-   
-   %  Create comparing axis
-   cmp   = length(unique(obj(1).pva.axcomp.feature));
-   if min(dsz)>1 
-      cmp = 1; 
-      if dsz(1)>dsz(2)
-         obj(1).pva.axcomp.orientation = 'vertical'; 
-      else
-         obj(1).pva.axcomp.orientation = 'horizontal';  
-      end
-   end
-   nObj  = numel(obj)*cmp;
-   
-   for iObj = 1:numel(obj)
-      % Repeat for comparing axis
-      for iCmp = 1:cmp
-         
-         %  Make Axes 
-         iAx      = pb_invidx([dsz(1), dsz(2)],iObj);
-         ax(iAx)  = subplot(dsz(1),dsz(2),iObj);
-
-         if obj(iAx).pva.subtitle; title(obj(iAx).pva.subtitle); end
-         axis(obj(iAx).pva.axis);
-         hold on;
-
-         % Set colors
-         nCol = 1;
-         if ~obj(iObj).pva.continious 
-            nCol = length(unique(obj(iObj).pva.color));
-         end
-
-         %  Plot all graphs
-         for iDP = 1:length(obj(iObj).dplot)
-            d 	= obj(iAx).pva;
-            obj(iObj).dplot{iDP}(obj,d);
-         end
-
-         %  Set labels
-         if ~obj(1).labels.supx; xlabel(obj(iAx).labels.xlab); end
-         if ~obj(1).labels.supy; ylabel(obj(iAx).labels.ylab); end
-
-         %  Make scientific notations on the axes.
-         ax(iAx).YAxis.Exponent = length(num2str(max(abs(round(ax(iAx).YLim)))))-1;
-         ax(iAx).XAxis.Exponent = length(num2str(max(abs(round(ax(iAx).XLim)))))-1;
-      end
-   end
-   
-   %% Adjust axis handles
-   %  Set super labels
-   
-   %  TO DO:
-   %  1. Optionalize subplots to have squared/linked/fixed axis
-   %  2. Scale and move axis to make graph nice, pleasing and non-overlapping
-   make_axes(obj,ax);
-   make_suplabel(obj);
-end
-
-
-% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
-%                                                           %
-%       Part of Programmeer Beer Toolbox (PBToolbox)        %
-%       Written by: Jesse J. Heckman (2019)                 %
-%                                                           %
-% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
\ No newline at end of file

subtools/draft/@pb_draft/pb_draft.m

@@ -50,21 +50,21 @@ classdef pb_draft < matlab.mixin.Copyable
       
       %  Set functions
       set_title(obj,title,varargin);            % set title
-      set_legend(obj,varargin);                 % set legend               /// NOT YET DONE
+      set_legend(obj,varargin);                 % set legend               
       set_labels(obj,varargin);                 % set labels
       set_grid(obj,varargin);                   % set grid
-      set_axcomp(obj,feature,varargin);         % set comparision axe      /// WORKING ON IT
+      set_axcomp(obj,feature,varargin);         % set comparision axe
       
       %  Plot functions
       plot_rawdata(obj,varargin);               % plot the rawdata
+      plot_bubble(obj,varargin);                % plot bubble histoplot
       plot_hline(obj,varargin);                 % plot horizontal lines
       plot_vline(obj,varargin);                 % plot vertical lines
-      plot_dline(obj,varargin);                 % plot diagonal lines
-      plot_bubble(obj,varargin);                % plot bubble histoplot
+      plot_dline(obj,varargin);                 % plot diagonal lines    
       
       %  Statistical functions
       stat_regres(obj,varargin);                % transform regression     // NOT YET DONE
-      stat_probit(obj,varargin);                % transform probit
+      stat_probit(obj,varargin);                % transform probit         // MADE NOT FINISHED
       
       %  Fitting functions
       fit_ellipse(obj,varargin);                % make ellipse fit

subtools/draft/@pb_draft/plot_rawdata.m

@@ -27,8 +27,6 @@ end
 function h = rawdata(~,data,p,colorindex)
    %  Plots rawdata
    
-   %% MAKE SELECTION FOR COLOR!
-   
    sel   = data.color == colorindex;
    x     = data.x(sel);
    y     = data.y(sel);

subtools/draft/@pb_draft/private/make_axes.m

@@ -8,19 +8,20 @@ function make_axes(obj,ax,varargin)
 % PBToolbox (2019): JJH: j.heckman@donders.ru.nl
    
    linkaxes(ax,'xy');
-   
    positions = zeros(length(ax),4);
    
    for iAx = 1:length(ax)
+      
       axis(ax(iAx));
-      xt    = xticks;
-      yt    = yticks;
+
+      % Set Limits
+      if obj(1).pva.setAxes
+         xlim(obj(1).pva.limits.x);
+         ylim(obj(1).pva.limits.y);
+      end
+
+      % Set Grids
       setAx = ax(iAx);
-      
-      xlim(ax(iAx),[xt(1) xt(end)]);
-      ylim(ax(iAx),[yt(1) yt(end)]);
-      positions(iAx,:) = ax(iAx).Position(:);
-      
       if obj(1).grid.bool
          f = obj(1).grid.features;
          setAx.Box           = f.Box;
@@ -36,12 +37,15 @@ function make_axes(obj,ax,varargin)
          setAx.YDir          = f.YDir;
          setAx.LineWidth     = f.LineWidth;
       end
+      positions(iAx,:) = ax(iAx).Position(:);
    end
    
+   % Set Label Positions
+   % TODO: THIS MUST BE DONE WAY BETTER!!
    obj(1).labels.ypos   = min(positions(:,2));
    obj(1).labels.xpos   = min(positions(:,1));
    obj(1).labels.pos    = [min(positions(:,1))/1.33 min(positions(:,2))/1.33 max(positions(:,1)+positions(:,3)) max(positions(:,2)+positions(:,4))];
-   obj(1).h_ax_plot = ax;
+   obj(1).h_ax_plot     = ax;
 end
 
  

subtools/draft/@pb_draft/private/parse_va.m

@@ -7,29 +7,38 @@ function parse_va(obj,varargin)
 % See also PB_DRAFT
 
 % PBToolbox (2018): JJH: j.heckman@donders.ru.nl
-
-   %% READ DATA
-   %  Read Data, and set keyvals
    
+   %% Initialize
    %  Read keyvals
+   
    v = varargin;
    pva.x             = pb_keyval('x',v,[]);
    pva.y             = pb_keyval('y',v,[]);
    pva.z             = pb_keyval('z',v,[]);
    pva.def           = pb_keyval('def',v,1);
-   pva.color         = pb_keyval('color',v,ones(length(pva.x),1));
+   pva.color         = pb_keyval('color',v,ones(length(pva.y),1));
    pva.axis          = pb_keyval('axis',v);
    pva.subtitle      = pb_keyval('subtitle',v);
    pva.linkax        = pb_keyval('link',v,true);
+   pva.setAxes       = pb_keyval('setaxes',v,true);
+   
+   %% Set Core
+   %  Read, check and set data.
    
    %  Check data limits
-   [x,y]             = setlim(pva); 
+   if isempty(pva.x); s = size(pva.y); pva.x = zeros(s(1),s(2)); end
+   
+   [x,y]   = setlim(pva);
+   if strcmp(pva.axis,'square') &&  x ~= y
+      x = [min([x y]) max([x y])];    
+      y = x;
+   end
    pva.limits.x      = x;
    pva.limits.y      = y;
    
    %  Check square axis
    if isempty(pva.axis)
-      if abs(max(x)-max(y)) / max([x,y])<.5
+      if abs(max(x)-max(y)) / max([x,y]) < 0.5
          pva.axis = 'square';
       end
    end
@@ -38,28 +47,33 @@ function parse_va(obj,varargin)
    pva.colscheme     = pb_selectcolor(length(unique(pva.color)),pva.def);
    pva.axcomp        = axcmp(pva.x);
    
+   %  Set Labels
    obj.labels.xlab   = pb_keyval('xlab',v,'');
    obj.labels.ylab   = pb_keyval('ylab',v,'');
    obj.grid.bool     = false;
    
    %  Check data continuity for colouring
    pva.continious = false;
-   if length(unique(pva.color))>5 && ~prod(floor(pva.color) == pva.color)
+   if length(unique(pva.color)) > 5 && ~prod(floor(pva.color) == pva.color)
       pva.continious = true;
    end
    
    obj.pva = pva;
 end
 
-function ac = axcmp(data)
+function axc = axcmp(data)
    %  Writes empty axcomp data struct
-   ac.prefix      = '';
-   ac.feature     = ones(1,length(data));
-   ac.n           = length(unique(ac.feature));
+   
+   axc.prefix      = '';
+   axc.feature     = ones(1,length(data));
+   axc.n           = length(unique(axc.feature));
 end
 
 function [x,y] = setlim(data)
    % Sets the limits for axes
+   
+   x = []; y = [];
+   
    x = [min(data.x) max(data.x)];
    y = [min(data.y) max(data.y)];
    
@@ -71,19 +85,19 @@ function [x,y] = setlim(data)
    if abs(min(y))/yr < .1; y(1) = 0; end
    
    % maximum
-   tmp      = max([x,y]);
+   maxD      = max([x,y]);
    order    = 0;
    scale    = .1;
    
-   if tmp<1; scale = 10; end
+   if maxD < 1; scale = 10; end
    
-   while tmp < .1 || tmp > 1
-      tmp = tmp*scale; 
+   while maxD < .1 || maxD > 1
+      maxD = maxD*scale; 
       order = order+1;
    end
-   tmp   = round(tmp*100)/100;
-   x(2)  = tmp * inv(scale)^order;
-   y(2)  = tmp * inv(scale)^order;
+   maxD   = round(maxD*100)/100;
+   x(2)  = maxD * inv(scale)^order;
+   y(2)  = maxD * inv(scale)^order;
 end
 
 

subtools/draft/@pb_draft/stat_probit.m

+function stat_probit(obj,varargin)
+% PB_DRAFT>PB_PROBIT
+%
+% Creates a probit plot.
+%
+% OBJ.STAT_PROBIT(varargin) plots RT data and transforms axes to the classic
+% probit display, i.e. cum. prob. vs promptness.
+%
+% See also PB_DRAFT, DRAFT, PB_PROBIT
+ 
+% PBToolbox (2019): JJH: j.heckman@donders.ru.nl
+   
+   v              = varargin;
+   p.ncol         = pb_keyval('ncol',v,unique(obj.pva.color));
+   p.visibility   = pb_keyval('visibility',v,'off');
+   
+   obj.plot_hline;
+   for iCol = 1:length(p.ncol)
+      obj.dplot   = vertcat(obj.dplot,{@(dobj,data)probit_stat(dobj,data,p,p.ncol(iCol))});
+   end
+   obj.results.rawdata_handle = {};
+   obj.pva.setAxes            = false;
+end
+
+function h = probit_stat(~,data,p,colorindex)
+   %% Initialize
+   %  Read and select data.
+   
+	sel   = data.color == colorindex;
+   y     = data.y(sel);
+   
+   if isempty(y); disp('No entry for y-data found!'); return; end
+   gcol  = pb_selectcolor(length(p.ncol),5);
+   color = pb_selectcolor(length(p.ncol),data.def);
+   color = color(colorindex,:);
+   
+
+	%% Rawdata
+   %  Plot rawdata
+
+   iRT   = 1/(y);
+   x     = -1./sort(y);
+   n     = numel(iRT);
+   y     = probitscale((1:n)./n);
+   %h(1)    = plot(x,y,'Color',gcol(colorindex,:),'Marker','o','MarkerFaceColor',gcol(colorindex,:),'LineStyle','None');
+
+	%% Quantiles & regression
+
+   p        = [1,2,5,10,25,50,75,90 95 98 99]/100;
+   xtick    = sort(-1./(150+[0 pb_oct2bw(50,-1:5)]));
+
+   prob     = sqrt(2) * erfinv(2*p - 1);
+   q        = -1./quantile(y,p);
+   b        = regstats(prob,q);
+   
+   rl       = regline(b.beta,'k--');
+   h     = plot(q,prob,'Color',color,'Marker','o','MarkerFaceColor',color,'LineStyle','None');
+   %set(h(1),'Tag','Rawdata');
+   set(h,'Tag','Probit model');
+   set(rl,'Tag','Graphical aid: regline');
+
+	%% Design
+   %  Set Axis for probit
+   
+   % TODO: --> FIGURE OUT WHY THE FUCK THERE IS NO VISUAL PROBIT MODEL?
+% 
+%    set(gca,'XTick',xtick,'XTickLabel',-1./xtick);
+%    set(gca,'YTick',prob,'YTickLabel',p*100);
+%    xlim([min(xtick) max(xtick)]);
+%    ylim([probit(0.1/100) probit(99.9/100)]);
+%    xlabel('Reaction time (ms)');
+%    ylabel('Cumulative probability');
+%    axis square;
+% 	box off
+end
+
+function chi = probitscale(cdf)
+   % creates a probitscale
+
+   chi    = sqrt(2) * erfinv(2*cdf - 1);
+end
+
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2019)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

subtools/draft/example_draft.m

@@ -4,48 +4,79 @@
 pb_clean;                  % Empty
 load('exD_saccade');       % load example data
 cfn = 0;                   % Initialize current figure number
-run = 2;                   % Set # of blocks to run
+run = 3;                   % Set # of blocks to run
 
-%% Block1:
-%  Make figure 1: Plot rawdata + bubbleplot
+%% Block 1:
+%  Make figure 1: Plot data
 
 if run>cfn
-   cfn = pb_newfig(cfn,'size',[0 0 17 12],'resize','off'); 
-   for i = 1:1
-      for j = 1:2
-         d(j,i) = pb_draft('x',Saccades.GazeLatency,'y',Saccades.HeadLatency,'color',Saccades.Modality);
-         d(j,i).set_labels('x','Gaze Latency (ms)','y','Head Latency (ms)');
-         if ~iseven(i*j)
-            d(j,i).plot_rawdata;
-         else
-            d(j,i).plot_bubble;  
-            d(j,i).fit_ellipse;
-         end
-         d(j,i).plot_dline;
-         d(j,i).plot_vline('type','mode');
-         d(j,i).plot_hline('type','mode');
+   %  Make figure & draft-obj
+   cfn   = pb_newfig(cfn,'size',[0 0 17 17],'ws','Docked'); 
+   d     = pb_draft('x',Saccades.GazeLatency,'y',Saccades.HeadLatency,'color',Saccades.Modality);
+   
+   %  Plots
+   d.plot_rawdata
+   d.plot_vline('type','mode');
+   d.plot_hline('type','mode');
+   
+   %  Layout
+   d.set_title('Saccade Latencies');
+   d.set_labels('x','Gaze Latency (ms)','y','Head Latency (ms)');
+   d.set_grid;
+   
+   %  Build
+   d.draft
+   %d.print
+end
+
+
+%% Block 2:
+%  Make figure 2: Plot rawdata + bubbleplot
+
+if run>cfn
+   %  Make figure
+   cfn = pb_newfig(cfn,'size',[0 0 17 12],'ws','Docked'); 
+   for iR = 1:2
+      %  Build draft-objs
+      d(iR,1) = pb_draft('x',Saccades.GazeLatency,'y',Saccades.HeadLatency,'color',Saccades.Modality);
+
+      %  Plots
+      if ~iseven(iR)
+         d(iR,1).plot_rawdata;
+      else
+         d(iR,1).plot_bubble;  
+         d(iR,1).fit_ellipse;
       end
+      d(iR,1).plot_dline;
+
+      %  Axis Layout
+      d(iR,1).set_labels('x','Gaze Latency (ms)','y','Head Latency (ms)');
    end
 
+   %  Figure Layout
    d.set_title('Saccade Latencies');
    d.set_axcomp(Saccades.Subject);
    d.set_grid;
+   
+   %  Build
    d.draft;
-   d.print('disp',true);
+   %d.print
 end
 
-%% Block2:
-%  Make figure 2: Plot rawdata + bubbleplot
+%% Block 3:
 
 if run>cfn
-   cfn   = pb_newfig(cfn,'size',[0 0 17 17],'resize','off'); 
-   d     = pb_draft('x',Saccades.GazeLatency,'y',Saccades.HeadLatency,'color',Saccades.Modality);
+   %  Make figure & draft-obj
+   cfn   = pb_newfig(cfn,'size',[0 0 17 17],'ws','Docked');
+   d     = pb_draft('y',Saccades.HeadLatency); %,'color',Saccades.Modality);
+   
+   d.stat_probit;
+   
+   d.set_title('Probit plot');
+   d.set_labels('x','Reaction Times (ms)','y','Cumulative Probability');
+   d.set_grid;
+   
+   %  Build
+   d.draft;
+   %d.print
 end
-
-
-%% Block3:
-
-if run>cfn
-   cfn   = pb_newfig(cfn,'size',[0 0 17 17],'resize','off'); 
-   d     = pb_draft('x',Saccades.GazeLatency,'y',Saccades.HeadLatency,'color',Saccades.Modality);
-end
\ No newline at end of file

utilities/statistics/pb_probit.m

@@ -22,7 +22,7 @@ function [h,D] = pb_probit(D, varargin)
    pb_selectaxis(ax);
    hold on;
 
-   D = fixArgIn(D); len = length(D);