Accumulated and verified updates

GraphicsPlotting/BreakPlot.m

@@ -1,5 +1,5 @@
 function h=BreakPlot(y_break_start,y_break_end,break_type,axes_handle)
-% BreakPlot(x,y,y_break_start,y_break_end,break_type)
+% BreakPlot(y_break_start,y_break_end,break_type)
 % Produces a plot who's y-axis skips to avoid unecessary blank space
 %axis_handle is obtained by get(gca).
 % 

GraphicsPlotting/DendrogramMatrix.m

@@ -14,7 +14,7 @@
 %
 % Recommended usage: [DC,order]=DendrogramMatrix(C);
 % To show matrix use : imagesc(DC); or pcolor(DC); - to show grid
-function [DC,order,clusters,h,Z]=DendrogramMatrix(C,varargin)
+function [DC,order,clusters,h,Z,cophenetDist]=DendrogramMatrix(C,varargin)
 %default options
 toPlotBinaryTree=0;
 figureHandle=[];
@@ -76,8 +76,10 @@
 %calculate euclidean distance
 Y=pdist(C,linkMetric);
 Z=linkage(Y,linkMethod);
-%C = cophenet(Z,Y);
-%I=inconsistent(Z,4);
+if nargout==6
+    [~,cophenetDist] = cophenet(Z,Y);
+end
+%I=inconsistent(Z);
 
 if strcmp(Orientation,'right')
     pO1=[1 3];

GraphicsPlotting/colormap2D.m

@@ -0,0 +1,79 @@
+function [CM,CMP,h]=colormap2D(varargin)
+parseObj = inputParser;
+addParameter(parseObj,'nIntensities',100,@isnumeric);
+addParameter(parseObj,'nColors',256,@isnumeric);
+addParameter(parseObj,'blackAddition',0,@isnumeric); %adds black to top color, 0 value gives only white
+addParameter(parseObj,'multiplicationFactor',8,@isnumeric);%[0-Inf] - makes rate of change stronger
+addParameter(parseObj,'additionFactor',1.8,@isnumeric);%[0 1]- the higher makes changes weaker in total
+addParameter(parseObj,'plotCartColorBar',1,@isnumeric);%plot a colorbar in cartesian coordinates
+addParameter(parseObj,'plotPolarColorBar',1,@isnumeric);%plot a colorbar in polar coordinates
+addParameter(parseObj,'plotPolarExample',0,@isnumeric);%plot a possible implementation of the color map on a polar plot
+addParameter(parseObj,'inputParams',0,@isnumeric); %if 1 plots the possible inputs to the function
+
+parseObj.parse(varargin{:});
+par=parseObj.Results;
+if parseObj.Results.inputParams
+    disp(par);
+    return;
+end
+
+CMap=hsv(par.nColors);
+cmapR_theta=repmat(CMap,[1 1 par.nIntensities]);
+M=[];M(1,:,1:par.nIntensities)=(par.additionFactor+(0:(par.nIntensities-1))/par.nIntensities).^par.multiplicationFactor;
+
+cmapR_theta=bsxfun(@times, cmapR_theta+par.blackAddition*ones(size(cmapR_theta)),M);
+cmapR_theta=(cmapR_theta-min(cmapR_theta(:)));
+cmapR_theta=cmapR_theta./max((cmapR_theta(:)));
+cmapR_theta=1-cmapR_theta;
+
+CM=permute(cmapR_theta,[1,3,2]);
+
+if par.plotCartColorBar
+    h.f=figure('Position',[200 200 100 800]);
+    h.h=axes;
+    image(CM);axis tight;
+    ylabel('Color');
+    xlabel('Intensity')
+end
+
+if par.plotPolarColorBar
+    [X,Y]=meshgrid(0.01:0.01:1,0.01:0.01:1);
+    X=X-0.5;Y=Y-0.5;
+
+    [theta,rho]=cart2pol(X,Y);
+    normTheta=floor(1+((theta+pi)/2/pi)*(par.nColors-1));
+    normRho=floor(1+(rho/0.5)*(par.nIntensities-1));
+    normRho(normRho>par.nIntensities)=1;
+    CMP=zeros(100,100,3);
+    p{1}=sub2ind(size(CM),normTheta(:),normRho(:),ones(numel(normRho),1));
+    p{2}=sub2ind(size(CM),normTheta(:),normRho(:),2*ones(numel(normRho),1));
+    p{3}=sub2ind(size(CM),normTheta(:),normRho(:),3*ones(numel(normRho),1));
+
+    CMP(:)=cat(3,CM(p{1}),CM(p{2}),CM(p{3}));
+
+    h.fP=figure('Position',[200 200 130 120]);
+    h.hP=axes;
+    image(CMP);axis tight equal off;
+end
+
+%
+if par.plotPolarExample
+    [nRC,~,nTC]=size(cmapR_theta);
+
+    fP=figure('Position',[200 200 130 115]);
+    hP=polaraxes;colormap(hP,'hsv');hold on;
+
+    nR=50;
+    nT=20;
+    R=1:nR;
+    Theta=1:nT;
+
+    for i=1:nR
+        for j=1:nT
+            %plot(R(i),Theta(j),'.','MarkerSize',20,'Color',  cmapR_theta( ceil(R(i)/nR*nRC), : , ceil(Theta(j)/nT*nTC) )  )
+            polarplot(R(i)/nR*2*pi,Theta(j),'.','MarkerSize',5,'Color',  cmapR_theta( ceil(R(i)/nR*nRC), : , ceil(Theta(j)/nT*nTC) )  )
+        end
+    end
+    title(['Mul=' num2str(par.multiplicationFactor) ', Add=' num2str(par.additionFactor)])
+    set(hP,'RTick',[]);
+end

GraphicsPlotting/myErrorBar.m

@@ -1,4 +1,4 @@
-function [h,hE,hB]=myErrorBar(x,y,dy,width,varargin);
+function [h,hE,hB]=myErrorBar(x,y,dy,width,varargin)
 %[hE,hB]=myErrorBar(x,y,dy,width,varargin)
 %width [0-1] - the width in normalize units of the relative fraction of the bar (e.g. width=1 -> error bar in size of bar), leave empty [] if needed.
 %[h,hE,hB]=myErrorBar(1:8,Int,Int+IntStd,0.4,'Bfacecolor',[0.3 0.3 0.3],'BLinewidth',5,'Ecolor','k');
@@ -76,7 +76,7 @@
 
 %update axis arguments
 set(h,'xtick',x);
-set(h,axisVarArgIn{:});
+axes(h,axisVarArgIn{:});
 
 
 

GraphicsPlotting/tmp2.m

@@ -0,0 +1,6 @@
+121.5                        35                     151.5                        65
+left 2 right
+
+ballCoordinates
+
+[0 0 143 100]