bug fixings for option colorBlindSafe

DomenicoPerrottaJRC · DomenicoPerrottaJRC · commit 620b91d6c7e4 · 2026-07-07T01:14:49.000+02:00
diff --git a/toolbox/+aux/computePCA.m b/toolbox/+aux/computePCA.m
@@ -2,7 +2,6 @@
     computePCA(Y,bsb,rownames,varnames,standardize,NumComponents,dispresults,plots,Latitude,Longitude,ShapeFile,smartEVchart,colorBlindSafe)
 % Compute all PCA quantities (this function is not intended to be called
 % directly)
-
 [n,v]=size(Y);
 if isempty(bsb)
     bsb=true(n,1);
@@ -145,43 +144,44 @@
     end
 elseif iscellstr(plots) || ischar(plots) %#ok<ISCLSTR>
     % Note that warning is suppressed because of routine convertStringsToChars
-    % Check whether input is a cell array of characters or a character array
+    % Check whether input is a cell array of characters or a character array 
     showPlots=string(plots);
 else
     error('FSDA:pcaFS:WrongInputOpt',['input argument plots can be either 0/1 false/true' newline 'or a cell array of characters or a string array or a character array'])
 end
 
-%% Explained variance through Pareto plot
-% Delete figure if it already exists
-if ismember("Explained",showPlots)
-    delete(findobj(0, 'type', 'figure','tag','pl_eigen'));
-    figure('Name','Explained variance','Tag','pl_eigen')
-    [h,axesPareto]=pareto(explained(:,1),namerows);
-    % h(1) refers to the bars h(2) to the line
-    if colorBlindSafe
-        h(1).FaceColor=aux.sequential_hcl_matlab(1);
-    else
-        h(1).FaceColor='g';
+    %% Explained variance through Pareto plot
+    % Delete figure if it already exists
+    if ismember("Explained",showPlots)
+        delete(findobj(0, 'type', 'figure','tag','pl_eigen'));
+        figure('Name','Explained variance','Tag','pl_eigen')
+        [h,axesPareto]=pareto(explained(:,1),namerows);
+        % h(1) refers to the bars h(2) to the line
+        if colorBlindSafe
+            h(1).FaceColor=aux.sequential_hcl_matlab(1);
+        else
+            h(1).FaceColor='g';
+        end
+        linelabels = string(round(100*h(2).YData/sumla,2));
+        text(axesPareto(2),h(2).XData,h(2).YData,linelabels,...
+            'Interpreter','none');
+        xlabel('Principal components')
+        ylabel('Explained variance')
     end
-    linelabels = string(round(100*h(2).YData/sumla,2));
-    text(axesPareto(2),h(2).XData,h(2).YData,linelabels,...
-        'Interpreter','none');
-    xlabel('Principal components')
-    ylabel('Explained variance')
-end
 
 %% Plot loadings
 if ismember("Loadings",showPlots)
+
+    xlabels = categorical(varnames,varnames);
+
     if colorBlindSafe
         [negColor,posColor] = aux.plotLoadingsDiverging(loadings, varnames, NumComponents, 'Loadings', 'pl_loadings');
     else
         negColor = 'r';
         posColor = 'b';
-        
+
         delete(findobj(0, 'type', 'figure','tag','pl_loadings'));
         figure('Name','Loadings','Tag','pl_loadings')
-    
-        xlabels = categorical(varnames,varnames);
 
         for i=1:NumComponents
             subplot(NumComponents,1,i)
@@ -266,7 +266,7 @@
                     'VerticalAlignment','bottom')
                 text(i, ax.YLim(1) - 0.05*diff(ax.YLim), string(b.XData(i)), ...
                     'HorizontalAlignment','center', 'VerticalAlignment','top', ...
-                    'Color', 'b', 'Parent', ax);
+                    'Color', 'b', 'Parent', ax); % DDD 'b' or 'k'?
             end
         end
 
@@ -340,9 +340,23 @@
 if ~isempty(Latitude) &&  ~isempty(Longitude)
     delete(findobj(0, 'type', 'figure','tag','pl_latlong'));
     figure('Name','geobubble','tag','pl_latlong')
-    aux.plotGeobubbleDiverging(Latitude, Longitude, score(:,1), score(:,2), ...
-        "Geobubble of all units", "First PC (size)", "Second PC (color)", ...
-        'MapLayout','maximized');
+
+    if colorBlindSafe
+        aux.plotGeobubbleDiverging(Latitude, Longitude, score(:,1), score(:,2), ...
+            "Geobubble of all units", "First PC (size)", "Second PC (color)", ...
+            'MapLayout','maximized');
+    else
+
+        % Divide the second PC into 4 classes
+        cate=discretize(score(:,2),linspace(min(score(:,2)),max(score(:,2)),4),'categorical');
+
+        % Add title and legend titles
+        gb=geobubble(Latitude,Longitude,score(:,1),cate,'Basemap','topographic','MapLayout','maximized');
+        gb.Title = "Geobubble of all units";
+        gb.SizeLegendTitle = "First PC (size)";
+        gb.ColorLegendTitle = "Second PC (color)";
+    end
+
 elseif ~isempty(Latitude) ||  ~isempty(Longitude)
     error('FSDA:pcaFS:WrongInputOpt','Both Latitude and Longitude must be given.');
 end
diff --git a/toolbox/+aux/diverging_hcl_matlab.m b/toolbox/+aux/diverging_hcl_matlab.m
@@ -38,33 +38,59 @@
 %       cmap = diverging_hcl_matlab(256);
 %       colormap(cmap); colorbar; caxis([-1 1]);
 
+% p = inputParser;
+% addParameter(p,'H1',260);
+% addParameter(p,'H2',12);
+% addParameter(p,'C1',80);
+% addParameter(p,'L1',30);
+% addParameter(p,'L2',95);
+% addParameter(p,'Power',1.5);
+% parse(p,varargin{:});
+% o = p.Results;
+% 
+% half = ceil(n/2);
+% t = linspace(1,0,half)';              % 1 at extreme, 0 at center
+% L = o.L2 - (o.L2-o.L1).*t.^o.Power;
+% C = o.C1.*t.^o.Power;
+% 
+% negHalf = local_hcl2rgb(o.H1*ones(half,1), C, L);   % extreme -> center
+% posHalf = local_hcl2rgb(o.H2*ones(half,1), C, L);   % extreme -> center
+% 
+% cmap = [negHalf; flipud(posHalf(2:end,:))];         % extreme -> center -> extreme
+% cmap = max(0, min(1, cmap));
+% 
+% if size(cmap,1) ~= n
+%     idx  = round(linspace(1, size(cmap,1), n));
+%     cmap = cmap(idx,:);
+% end
+% end
+
+
 p = inputParser;
-addParameter(p,'H1',260);
-addParameter(p,'H2',12);
+addParameter(p,'H1',260);   % negative extreme hue (blue)
+addParameter(p,'H2',12);    % positive extreme hue (red)
 addParameter(p,'C1',80);
 addParameter(p,'L1',30);
 addParameter(p,'L2',95);
 addParameter(p,'Power',1.5);
 parse(p,varargin{:});
 o = p.Results;
 
-half = ceil(n/2);
-t = linspace(1,0,half)';              % 1 at extreme, 0 at center
-L = o.L2 - (o.L2-o.L1).*t.^o.Power;
-C = o.C1.*t.^o.Power;
+t = linspace(-1, 1, n)';        % -1 = negative extreme, 0 = center, 1 = positive extreme
+absT = abs(t);
 
-negHalf = local_hcl2rgb(o.H1*ones(half,1), C, L);   % extreme -> center
-posHalf = local_hcl2rgb(o.H2*ones(half,1), C, L);   % extreme -> center
+L = o.L2 - (o.L2 - o.L1) .* absT.^o.Power;
+C = o.C1 .* absT.^o.Power;
 
-cmap = [negHalf; flipud(posHalf(2:end,:))];         % extreme -> center -> extreme
-cmap = max(0, min(1, cmap));
+H = zeros(n,1);
+H(t < 0) = o.H1;
+H(t >= 0) = o.H2;
 
-if size(cmap,1) ~= n
-    idx  = round(linspace(1, size(cmap,1), n));
-    cmap = cmap(idx,:);
-end
+cmap = local_hcl2rgb(H, C, L);
+cmap = max(0, min(1, cmap));
 end
 
+
 function rgb = local_hcl2rgb(H, C, L)
 
 % Polar LUV (H,C,L) -> LUV -> CIEXYZ -> linear sRGB -> gamma-corrected sRGB
diff --git a/toolbox/+aux/plotGeobubbleDiverging.m b/toolbox/+aux/plotGeobubbleDiverging.m
@@ -17,13 +17,17 @@
 
 edges = linspace(min(colorVar), max(colorVar), 4);
 cate = discretize(colorVar, edges, 'categorical');
-cate = reordercats(cate, string(categories(cate)));  % ensure numeric bin order
+cate = reordercats(cate, string(categories(cate)));
+
+nCats = numel(categories(cate));
 
 gb = geobubble(lat, lon, sizeVar, cate, ...
     'Basemap','topographic', ...
     varargin{:});
-gb.BubbleColorList   = diverging_hcl_matlab(3);
+gb.BubbleColorList   = aux.diverging_hcl_matlab(nCats);   % always matches actual category count
 gb.Title             = titleStr;
 gb.SizeLegendTitle   = sizeLegend;
 gb.ColorLegendTitle  = colorLegend;
 end
+
+
diff --git a/toolbox/graphics/biplotAPP.mlapp b/toolbox/graphics/biplotAPP.mlapp
diff --git a/toolbox/graphics/geoplotAPP.mlapp b/toolbox/graphics/geoplotAPP.mlapp
diff --git a/toolbox/graphics/pcaProjection.m b/toolbox/graphics/pcaProjection.m
@@ -177,6 +177,15 @@ function pcaProjection(Y,varargin)
 LineWidthAxes=3;
 TextDensityPercentage =60;
 
+% Okabe–Ito is a colorblind-safe qualitative palette used by Zeileis et al. (2020)
+okabeIto = [0.00 0.45 0.70;   % blue
+            0.90 0.60 0.00;   % orange
+            0.00 0.62 0.45;   % bluish green
+            0.80 0.40 0.70;   % reddish purple
+            0.94 0.89 0.26;   % yellow
+            0.84 0.37 0.00;   % vermillion
+            0.35 0.35 0.35];  % gray (fallback for extra groups)
+
 if nargin>1
     options=struct('standardize',standardize,...
         'conflev',conflev,'AddAxes',AddAxes,'LineWidthAxes',LineWidthAxes,...
@@ -295,7 +304,7 @@ function pcaProjection(Y,varargin)
 
 for j=1:3
     if AddAxes(j) == true
-        addLinePCj(V,Xtilde,j,LineWidthAxes,TextAnToolbox);
+        addLinePCj(V,Xtilde,j,LineWidthAxes,TextAnToolbox,okabeIto(j,:));
     end
 end
 
@@ -316,7 +325,8 @@ function pcaProjection(Y,varargin)
 
 for j=1:3
     if AddAxes(j) == true
-        addLinePCj(V,Xtilde,1,LineWidthAxes,TextAnToolbox)
+        % DDD bug? is it V,Xtilde,1 or V,Xtilde,j ?
+        addLinePCj(V,Xtilde,1,LineWidthAxes,TextAnToolbox,okabeIto(j,:))
     end
 end
 
@@ -343,7 +353,7 @@ function pcaProjection(Y,varargin)
 hold('on')
 for j=1:3
     if AddAxes(j) == true
-        addLinePCj(V,Xtilde,j,LineWidthAxes,TextAnToolbox);
+        addLinePCj(V,Xtilde,j,LineWidthAxes,TextAnToolbox,okabeIto(j,:));
     end
 end
 
@@ -445,7 +455,7 @@ function pcaProjection(Y,varargin)
 
 for j=1:3
     if isMatlab && AddAxes(j) == true
-        addLinePCj(V,XX1,j,LineWidthAxes,TextAnToolbox);
+        addLinePCj(V,XX1,j,LineWidthAxes,TextAnToolbox,okabeIto(j,:));
     end
 end
 
@@ -456,30 +466,26 @@ function pcaProjection(Y,varargin)
 
 end
 
-function addLinePCj(V,Xtilde,j,lwd,TextAnToolbox)
+
+function addLinePCj(V,Xtilde,j,lwd,TextAnToolbox,axColor)
 vj=V(:,j);
 Xhatj = Xtilde*(vj*vj');
-% Take two points to draw this line
 [~,indminXj] = min(Xhatj(:,2));
 [~,indmaxXj] = max(Xhatj(:,2));
 
-% Add the line associated with jth PC
 line([Xhatj(indminXj,1); Xhatj(indmaxXj,1)], [Xhatj(indminXj,2); Xhatj(indmaxXj,2)], ...
-    [Xhatj(indminXj,3); Xhatj(indmaxXj,3)],'LineWidth',lwd);
+    [Xhatj(indminXj,3); Xhatj(indmaxXj,3)],'LineWidth',lwd,'Color',axColor);
 
 if TextAnToolbox ==true
-
     signindmaxXj=sign([Xhatj(indmaxXj,1); Xhatj(indmaxXj,2);  Xhatj(indmaxXj,3) ]);
-
     if isequal(sign(vj),signindmaxXj)
         textscatter3(Xhatj(indmaxXj,1), Xhatj(indmaxXj,2), ...
-            Xhatj(indmaxXj,3),"PC"+j);
+            Xhatj(indmaxXj,3),"PC"+j,'ColorData',axColor);
     else
         textscatter3(Xhatj(indminXj,1), Xhatj(indminXj,2), ...
-            Xhatj(indminXj,3),"PC"+j);
+            Xhatj(indminXj,3),"PC"+j,'ColorData',axColor);
     end
 end
-
 end
 
 function add3Daxes(j,color,lwd)
diff --git a/toolbox/graphics/scatterboxplot.m b/toolbox/graphics/scatterboxplot.m
@@ -91,6 +91,7 @@
 % the number of groups before calling scatterhist, so both the scatter and
 % the boxplot color inherit it consistently.
 
+% Okabe–Ito is a colorblind-safe qualitative palette used by Zeileis et al. (2020)
 okabeIto = [0.00 0.45 0.70;   % blue
             0.90 0.60 0.00;   % orange
             0.00 0.62 0.45;   % bluish green
diff --git a/toolbox/multivariate/pcaFS.m b/toolbox/multivariate/pcaFS.m
@@ -395,7 +395,7 @@
         'dispresults',dispresults,'NumComponents',NumComponents,...
         'robust',robust,'Latitude',Latitude,'Longitude',Longitude, ...
         'ShapeFile',ShapeFile,'smartEVchart',smartEVchart,...
-        'colorBlindSafe',false);
+        'colorBlindSafe',colorBlindSafe);
 
     [varargin{:}] = convertStringsToChars(varargin{:});
     UserOptions=varargin(1:2:length(varargin));
