Fixed bootstrap tests and included BCa and percentile confidence intervals

Engines/RDMcolormap.m → +rsa/+fig/RDMcolormap.m

@@ -5,6 +5,15 @@
 %__________________________________________________________________________
 % Copyright (C) 2012 Medical Research Council
 
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
+
 nCols = 256;
 %% blue-cyan-gray-red-yellow with increasing V (BCGRYincV)
 anchorCols=[0 0 1
@@ -26,4 +35,6 @@
 % figure(1); colormap(cols);
 % cm=colormap; hsvcm=rgb2hsv(cm);
 % subplot(3,1,3); cla; plot(brightness(colormap),'r'); hold on; plot(hsvcm(:,3),'k'); axis tight; legend({'brightness','V'});
-% th=addHeading('blue-cyan-gray-red-yellow with increasing V');
+% th=addHeading('blue-cyan-gray-red-yellow with increasing V');
+
+end%function

+rsa/+fig/addComparisonBars.m

@@ -0,0 +1,52 @@
+% this function adds the pairwise copmparison bars to a figure; the 'hold on'
+% should have been set before executing this function
+
+% pairWisePs: an nxn pairwise comparison matrix. This is supposed to be
+% sorted in descending order of average values (large to small heights)
+% a horizontal bar would be displayed whenever the (one-sided) comparison 
+% reaches a threshold.
+% HN, May 2013
+%__________________________________________________________________________
+% Copyright (C) 2012 Medical Research Council
+
+function y = addComparisonBars(pairwisePs,cYMax,threshold)
+
+    import rsa.*
+    import rsa.fig.*
+    import rsa.rdm.*
+    import rsa.stat.*
+    import rsa.util.*
+
+
+    nTestRDMs = size(pairwisePs,1);
+    eachLineHeight = 0.03;
+
+    padding = 2;
+
+    % Set `y` here in case no comparisons are significant.
+    y = cYMax;
+
+
+    nSignificantComparison = 0;
+    pairwiseI = 0;
+    for i = 1:nTestRDMs
+        for j = i+1:nTestRDMs
+
+            % The p value for i (the lower bar) being significantly smaller than j (the higher bar) is the p value for j being significantly higher than i. This is pairwisePs(j,i) (the lt?)
+            thisPairwiseP = pairwisePs(i,j);
+
+            if thisPairwiseP <= threshold
+                y = cYMax;
+                pairwiseI = pairwiseI + 1;
+                xx = [i j];
+
+                y = y + (cYMax * eachLineHeight * padding / 2); %padding
+                y = y + (pairwiseI * eachLineHeight * cYMax); %line separation
+                yy = [y y];
+                line(xx, yy, 'LineStyle', '-', 'LineWidth', 2, 'Marker', 'none', 'Color', [0 0 0]);
+                nSignificantComparison = nSignificantComparison + 1;
+
+            end%if
+        end%for:j
+    end%for:i
+end%function

Engines/addHeading.m → +rsa/+fig/addHeading.m

@@ -2,6 +2,15 @@ function addHeading(heading,figI,x,y)
 % adds a heading to a figure. The user also has the option of specifying
 % the location of the inserted heading text.
 
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
+
 % replace underscores
 if iscell(heading)
     for lineI=1:numel(heading)
@@ -13,7 +22,10 @@ function addHeading(heading,figI,x,y)
     heading(heading==95)='-';
 end    
 
-if ~exist('figI','var'), figI=gcf; end
+if ~exist('figI','var')
+    newFigure = gcf;
+    figI=newFigure.Number;
+end
 pageFigure(figI);
 
 if ~exist('x','var'), x=1.11; end
@@ -25,3 +37,5 @@ function addHeading(heading,figI,x,y)
 
 % add heading(s)
 text(x,y,heading,'HorizontalAlignment','Right','VerticalAlignment','Top','FontSize',12,'FontWeight','bold','Color','k');
+
+end%function

Engines/addImageSequenceToAxes.m → +rsa/+fig/addImageSequenceToAxes.m

@@ -18,6 +18,16 @@ function addImageSequenceToAxes(ax,il)
 % transparentCol is left out here
 %__________________________________________________________________________
 % Copyright (C) 2010 Medical Research Council
+
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
+
 defaultil = struct('sequence',1:length(il.images),'nRows',2, ...
 	'blackdisks',false);
 
@@ -208,3 +218,5 @@ function addImageSequenceToAxes(ax,il)
 oldy = get(ax,'ylim');
 set(ax,'xlim',oldx * padding);
 set(ax,'ylim',oldy * padding);
+
+end%function

Engines/colorScale.m → +rsa/+fig/colorScale.m

@@ -4,6 +4,14 @@
 %__________________________________________________________________________
 % Copyright (C) 2012 Medical Research Council
 
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 
 %% preparations
 if ~exist('monitor','var'), monitor=false; end
@@ -20,4 +28,4 @@
     imagesc(reshape(cols,[nCols 1 3]));
 end
 
-
+end%function

Engines/exportCurrentFigAsPDF.m → +rsa/+fig/exportCurrentFigAsPDF.m

@@ -8,6 +8,14 @@ function exportCurrentFigAsPDF(filespec,userOptions)
 %__________________________________________________________________________
 % Copyright (C) 2009 Medical Research Council
 
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 
 if ~isfield(userOptions,'dpi'), userOptions.dpi = 300; end;
 if ~isfield(userOptions,'tightInset'), userOptions.tightInset = false; end;
@@ -25,4 +33,6 @@ function exportCurrentFigAsPDF(filespec,userOptions)
     case 3
         print('-dpdf',sprintf('-r%d',userOptions.dpi),[filespec,'_',num2str(gcf)]);
         print('-dpdf',sprintf('-r%d',userOptions.dpi),'-append',filespec);
-end
+end
+
+end%function

Engines/exportCurrentFigAsPostscript.m → +rsa/+fig/exportCurrentFigAsPostscript.m

@@ -10,6 +10,15 @@ function exportCurrentFigAsPostscript(filespec,appendFlag,userOptions)
 %__________________________________________________________________________
 % Copyright (C) 2010 Medical Research Council
 
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
+
 if ~exist('filespec','var'), filespec='currentFigAsPostscript'; end;
 if ~exist('appendFlag','var'), appendFlag=1; end;
 if ~isfield(userOptions,'dpi'), userOptions.dpi = 300; end;
@@ -31,4 +40,6 @@ function exportCurrentFigAsPostscript(filespec,appendFlag,userOptions)
     case 4
         print('-dpsc2',sprintf('-r%d',userOptions.dpi),filespec);
         print('-dpsc2',sprintf('-r%d',userOptions.dpi),'-append','^ALL_POSTSCRIPTS_appendFlag4');
-end
+end
+
+end%function

Engines/exportfig.m → +rsa/+fig/exportfig.m

@@ -88,6 +88,14 @@ function exportfig(varargin)
 %       text in 10 point fonts. The size of the exported figure is
 %       the figure's PaperPostion width and height.
 
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 
 if (nargin < 2)
   error('Too few input arguments');
@@ -405,24 +413,59 @@ function exportfig(varargin)
 %
 
 function outData = LocalPushOldData(inData, objs, prop, values)
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 outData.objs = {inData.objs{:}, objs};
 outData.prop = {inData.prop{:}, prop};
 outData.values = {inData.values{:}, values};
+end%function
 
 function cellArray = LocalGetAsCell(fig,prop);
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 cellArray = get(fig,prop);
 if (~isempty(cellArray)) & (~iscell(cellArray))
   cellArray = {cellArray};
 end
+end%function
 
 function newArray = LocalScale(inArray, scale, minValue)
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 n = length(inArray);
 newArray = cell(n,1);
 for k=1:n
   newArray{k} = max(minValue,scale*inArray{k}(1));
 end
+end%function
 
 function newArray = LocalMapToGray(inArray);
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 n = length(inArray);
 newArray = cell(n,1);
 for k=1:n
@@ -460,8 +503,17 @@ function exportfig(varargin)
     newArray{k} = [color color color];
   end
 end
+end%function
 
 function newArray = LocalMapCData(inArray);
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 n = length(inArray);
 newArray = cell(n,1);
 for k=1:n
@@ -474,8 +526,17 @@ function exportfig(varargin)
   end
   newArray{k} = color;
 end
+end%function
 
 function outData = LocalUpdateColors(inArray, prop, inData)
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 value = LocalGetAsCell(inArray,prop);
 outData.objs = {inData.objs{:}, inArray};
 outData.prop = {inData.prop{:}, {prop}};
@@ -488,13 +549,32 @@ function exportfig(varargin)
   end
   set(inArray,{prop},value);
 end
+end%function
 
 function bool = LocalIsPositiveScalar(value)
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 bool = isnumeric(value) & ...
        prod(size(value)) == 1 & ...
        value > 0;
+end%function
 
 function value = LocalToNum(value)
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
 if ischar(value)
   value = str2num(value);
 end
+end%function

Engines/figureDendrogram.m → +rsa/+fig/figureDendrogram.m

@@ -43,6 +43,15 @@ function figureDendrogram(RDM, userOptions, localOptions)
 %__________________________________________________________________________
 % Copyright (C) 2010 Medical Research Council
 
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
+
 if ~isfield(localOptions, 'linkageType')
 	localOptions.linkageType = 'single';
 end
@@ -75,3 +84,5 @@ function figureDendrogram(RDM, userOptions, localOptions)
 fileName = [userOptions.analysisName '_' localOptions.fileName];
 handleCurrentFigure(fileName, userOptions);
 clear thisFileName
+
+end%function

Engines/figureMDSArrangement.m → +rsa/+fig/figureMDSArrangement.m

@@ -93,6 +93,15 @@ function figureMDSArrangement(RDM, userOptions, localOptions)
 %__________________________________________________________________________
 % Copyright (C) 2010 Medical Research Council
 
+import rsa.*
+import rsa.fig.*
+import rsa.fmri.*
+import rsa.rdm.*
+import rsa.sim.*
+import rsa.spm.*
+import rsa.stat.*
+import rsa.util.*
+
 %% define defaults
 appendFlag = 0;
 % warning('off', 'IgnoringExtraEntries');
@@ -237,6 +246,8 @@ function figureMDSArrangement(RDM, userOptions, localOptions)
 	clear thisFileName
 end
 
+end%function
+
 
 % %% plot MDS arrangement using category-color-coded dots
 % if isfield(options,'figI_catCols')&&~isempty(options.figI_catCols) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%