clusterDistances.m
1bf6e83009cemaster

clusterDistances.m
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			function clusterDistances( spotData, clusterIndexes, zComp, minDist, parent )

			global X;
			color = createLUT(max(clusterIndexes), 255);
			for clus = 1:max(clusterIndexes)

			% Get indices of spots belonging to cluster clus
			clusInd = find(clusterIndexes == clus);
			nSpots(clus) = numel(clusInd);


			spotPositions = spotData.posXYZ(clusInd,:);
			% Cluster could be empty
			if ~isempty(spotPositions)

			clusterSpotsFolder = X.CreateGroup(sprintf('Cluster %d', clus));
			X.AddToScene(clusterSpotsFolder, 'Parent', parent);
			% compensate Z
			spotPositions(:,3) = spotPositions(:,3) / zComp;

			% Easy to get subclusters by distance
			if size(spotPositions, 1) > 1
			T = clusterdata(spotPositions,'criterion', 'distance', 'distance', 'euclidean', 'cutoff', minDist);
			else
			T = 1;
			end

			% Get the IDs for each cluster and make a spot
			subclusIds = unique(T);
			for subClus = subclusIds'
			idx = find(T==subClus);
			tempSpot = X.CreateSpots(spotData.posXYZ(clusInd(idx),:), spotData.radii(clusInd(idx),1)', 'Name', sprintf('Subcluster %d', subClus));
			X.SetColor(tempSpot, color(clus,:));
			X.AddToScene(tempSpot, 'Parent',clusterSpotsFolder);
			end
			ns=length(subclusIds);

			disp(sprintf(' Cluster %d: %d Subclusters: %d Spots', clus, ns, nSpots(clus)));
			end
			end


			end