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POK-means Plotting for 3 Dimensional Data
 

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  1. POK-means Plotting for 3 Dimensional Data
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    <p>I'm working with k-means in MATLAB. I am trying to create the plot/graph, but my data has three dimensional array. Here is my k-means code:</p> <pre><code>clc clear all close all load cobat.txt; % read the file k=input('Enter a number: '); % determine the number of cluster isRand=0; % 0 -&gt; sequeantial initialization % 1 -&gt; random initialization [maxRow, maxCol]=size(cobat); if maxRow&lt;=k, y=[m, 1:maxRow]; elseif k&gt;7 h=msgbox('cant more than 7'); else % initial value of centroid if isRand, p = randperm(size(cobat,1)); % random initialization for i=1:k c(i,:)=cobat(p(i),:); end else for i=1:k c(i,:)=cobat(i,:); % sequential initialization end end temp=zeros(maxRow,1); % initialize as zero vector u=0; while 1, d=DistMatrix3(cobat,c); % calculate the distance [z,g]=min(d,[],2); % set the matrix g group if g==temp, % if the iteration doesn't change anymore break; % stop the iteration else temp=g; % copy the matrix to the temporary variable end for i=1:k f=find(g==i); if f % calculate the new centroid c(i,:)=mean(cobat(find(g==i),:),1); end end c [B,index] = sortrows( c ); % sort the centroids g = index(g); % arrange the labels based on centroids end y=[cobat,g] hold off; %This plot is actually placed in plot 3D code (last line), but I put it into here, because I think this is the plotting line f = PlotClusters(cobat,g,y,Colors) %Here is the error if Dimensions==2 for i=1:NumOfDataPoints %plot data points plot(cobat(i,1),cobat(i,2),'.','Color',Colors(g(i),:)) hold on end for i=1:NumOfCenters %plot the centers plot(y(i,1),y(i,2),'s','Color',Colors(i,:)) end else for i=1:NumOfDataPoints %plot data points plot3(cobat(i,1),cobat(i,2),cobat(i,3),'.','Color',Colors(g(i),:)) hold on end for i=1:NumOfCenters %plot the centers plot3(y(i,1),y(i,2),y(i,3),'s','Color',Colors(i,:)) end end end </code></pre> <p>And here is the plot 3D code:</p> <pre><code>%This function plots clustering data, for example the one provided by %kmeans. To be able to plot, the number of dimensions has to be either 2 or %3. %Inputs: % Data - an m-by-d matrix, where m is the number of data points to % cluster and d is the number of dimensions. In my code, it is cobat % IDX - an m-by-1 indices vector, where each element gives the % cluster to which the corresponding data point in Data belongs. In my file, it is 'g' % Centers y - an optional c-by-d matrix, where c is the number of % clusters and d is the dimensions of the problem. The matrix % gives the location of the cluster centers. If this is not % given, the centers will be calculated. In my file, I think, it is 'y' % Colors - an optional color scheme generated by hsv. If this is not % given, a color scheme will be generated. % function f = PlotClusters(cobat,g,y,Colors) %Checking inputs switch nargin case 1 %Not enough inputs error('Clustering data is required to plot clusters. Usage: PlotClusters(Data,IDX,Centers,Colors)') case 2 %Need to calculate cluster centers and color scheme [NumOfDataPoints,Dimensions]=size(cobat); if Dimensions~=2 &amp;&amp; Dimensions~=3 %Check ability to plot error('It is only possible to plot in 2 or 3 dimensions.') end if length(g)~=NumOfDataPoints %Check that each data point is assigned to a cluster error('The number of data points in Data must be equal to the number of indices in IDX.') end NumOfClusters=max(g); Centers=zeros(NumOfClusters,Dimensions); NumOfCenters=NumOfClusters; NumOfPointsInCluster=zeros(NumOfClusters,1); for i=1:NumOfDataPoints Centers(g(i),:)=y(g(i),:)+cobat(i,:); NumOfPointsInCluster(g(i))=NumOfPointsInCluster(g(i))+1; end for i=1:NumOfClusters y(i,:)=y(i,:)/NumOfPointsInCluster(i); end Colors=hsv(NumOfClusters); case 3 %Need to calculate color scheme [NumOfDataPoints,Dimensions]=size(cobat); if Dimensions~=2 &amp;&amp; Dimensions~=3 %Check ability to plot error('It is only possible to plot in 2 or 3 dimensions.') end if length(g)~=NumOfDataPoints %Check that each data point is assigned to a cluster error('The number of data points in Data must be equal to the number of indices in IDX.') end NumOfClusters=max(g); [NumOfCenters,Dims]=size(y); if Dims~=Dimensions error('The number of dimensions in Data should be equal to the number of dimensions in Centers') end if NumOfCenters&lt;NumOfClusters %Check that each cluster has a center error('The number of cluster centers is smaller than the number of clusters.') elseif NumOfCenters&gt;NumOfClusters %Check that each cluster has a center disp('There are more centers than clusters, all will be plotted') end Colors=hsv(NumOfCenters); case 4 %All data is given just need to check consistency [NumOfDataPoints,Dimensions]=size(cobat); if Dimensions~=2 &amp;&amp; Dimensions~=3 %Check ability to plot error('It is only possible to plot in 2 or 3 dimensions.') end if length(g)~=NumOfDataPoints %Check that each data point is assigned to a cluster error('The number of data points in Data must be equal to the number of indices in IDX.') end NumOfClusters=max(g); [NumOfCenters,Dims]=size(y); if Dims~=Dimensions error('The number of dimensions in Data should be equal to the number of dimensions in Centers') end if NumOfCenters&lt;NumOfClusters %Check that each cluster has a center error('The number of cluster centers is smaller than the number of clusters.') elseif NumOfCenters&gt;NumOfClusters %Check that each cluster has a center disp('There are more centers than clusters, all will be plotted') end [NumOfColors,RGB]=size(Colors); if RGB~=3 || NumOfColors&lt;NumOfCenters error('Colors should have at least the same number of rows as number of clusters and 3 columns') end end %Data is ready. Now plotting end </code></pre> <p>Here is the error:</p> <pre><code>??? Undefined function or variable 'Colors'. Error in ==&gt; clustere at 69 f = PlotClusters(cobat,g,y,Colors) </code></pre> <p>Am I wrong call the function like that? What should I do? Your help will be appreciated a lot.</p>
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    1. USAmro
    1. USAlvi Syahrin
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    1. COyou never defined the `Colors` variable, hence the error message..
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      1. USAmro
    2. CONow I define Colors, like this: `Colors=['r' 'g' 'b' 'c' 'm' 'y' 'k'];` is it right? But now I got another error: `Error in ==> PlotClusters at 22 switch nargin ??? Output argument "f" (and maybe others) not assigned during call to "E:\MATLAB 2012\PlotClusters.m>PlotClusters". Error in ==> clustere at 68 f = PlotClusters(cobat,g,y,Colors)` Thank you so much, @Amro, for always helping me. Your help means a lot and I always appreciate it.
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      1. POK-means Plotting for 3 Dimensional Data
      1. USAlvi Syahrin
    3. COyour code has a number of problems. Rather than going through each, I provided my own example. Please study it and adapt it to your case.
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      1. POK-means Plotting for 3 Dimensional Data
      1. USAmro
 

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