Daniel@0: function h = som_clplot(sC,varargin)
Daniel@0: 
Daniel@0: %SOM_CLPLOT Visualize clustering.
Daniel@0: % 
Daniel@0: % h = som_clplot(sC, [[argID,] value, ...])
Daniel@0: % som_clplot(sM, part)
Daniel@0: % 
Daniel@0: %   som_clplot(sC);
Daniel@0: %   som_clplot(som_clstruct(Z))
Daniel@0: %   som_clplot(sC,sM);
Daniel@0: %   som_clplot(sC,'coord',P);
Daniel@0: %   som_clplot(sC,'dendrogram',[1 1 1 1 0 0 1 1 0 0 1]);
Daniel@0: %   som_clplot(sC,'linewidth',10);
Daniel@0: %   som_clplot(sC,'size',10);
Daniel@0: %   som_clplot(sM,part);
Daniel@0: %    
Daniel@0: %  Input and output arguments ([]'s are optional):    
Daniel@0: %   sC        (struct) clustering struct, as produced by SOM_CLSTRUCT
Daniel@0: %   [argID,   (string) See below. Each pair is the fieldname and 
Daniel@0: %    value]   (varies) the value to be given to that field.
Daniel@0: %   sM        (struct) map struct
Daniel@0: %   part      (vector) length = munits, partitioning for the map
Daniel@0: %
Daniel@0: %   h         (vector) handles to the arcs between 
Daniel@0: %   
Daniel@0: % Here are the valid argument IDs and corresponding values. The values 
Daniel@0: % which are unambiguous (marked with '*') can be given without the
Daniel@0: % preceeding argID.
Daniel@0: %   'linecolor' (string) color of the arc lines, 'k' by default
Daniel@0: %               (vector) size 1 x 3
Daniel@0: %   'linewidth' (scalar) width of the arc lines
Daniel@0: %   'size'      (vector) length 2*clen-1, sizes for each of the 
Daniel@0: %                        cluster markers
Daniel@0: %               (scalar) this size is used for all cluster markers
Daniel@0: %   'dendrogram'(vector) size 2*clen-1, indicates which clusters 
Daniel@0: %                        are shown in the dendrogram
Daniel@0: %              *(string) 'on' or 'off' ('on' by default)
Daniel@0: %   'coord'     (matrix) size dlen x odim, the coordinates
Daniel@0: %                        for the data. If odim<=2, these are used as is.
Daniel@0: %                        Otherwise a 2-dimensional PCA-projection is
Daniel@0: %                        first made (see function PCAPROJ). These
Daniel@0: %                        coordinates are applied also to the clusters.
Daniel@0: %              *(struct) data struct: as above
Daniel@0: %                        map or topology struct: the coordinates given 
Daniel@0: %                        by SOM_VIS_COORDS are used for the data 
Daniel@0: %   'color'     (matrix) size dlen x 3, color for each data. By
Daniel@0: %                        default the colors defined for base 
Daniel@0: %                        clusters are used (sC.color(sC.base,:)).
Daniel@0: %                        For ignored data figure background color is used. 
Daniel@0: %               (vector) size dlen x 1, indexed colors are used
Daniel@0: %
Daniel@0: % See also SOM_CLSTRUCT, SOM_LINKAGE, SOM_CLPRUNE, LINKAGE, DENDROGRAM.
Daniel@0: 
Daniel@0: % Copyright (c) 2000 by Juha Vesanto
Daniel@0: % Contributed to SOM Toolbox on XXX by Juha Vesanto
Daniel@0: % http://www.cis.hut.fi/projects/somtoolbox/
Daniel@0:  
Daniel@0: % Version 2.0beta juuso 180600
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %% read the arguments
Daniel@0: 
Daniel@0: % sC
Daniel@0: if strcmp(sC.type,'som_map'), 
Daniel@0:   base = varargin{1}; 
Daniel@0:   clen = length(unique(base(isfinite(base)))); 
Daniel@0:   Z = ones(clen-1,3); 
Daniel@0:   Z(:,1) = randperm(clen-1)'; 
Daniel@0:   Z(:,2) = [clen:2*clen-2]'; 
Daniel@0:   Z(:,3) = [1:clen-1]'; 
Daniel@0:   sT = sC;
Daniel@0:   sC = som_clstruct(Z,'base',varargin{1}); 
Daniel@0:   h = som_clplot(sC,'coord',sT,'dendrogram','off',varargin{2:end}); 
Daniel@0:   return; 
Daniel@0: end
Daniel@0: clen = size(sC.tree,1)+1; 
Daniel@0: 
Daniel@0: % varargin
Daniel@0: show = 'on'; 
Daniel@0: markersize = 10; 
Daniel@0: linecolor = 'k'; 
Daniel@0: linewidth = 1; 
Daniel@0: datacoord = []; 
Daniel@0: datacolor = []; 
Daniel@0: 
Daniel@0: i=1; 
Daniel@0: while i<=length(varargin), 
Daniel@0:   argok = 1; 
Daniel@0:   if ischar(varargin{i}), 
Daniel@0:     switch varargin{i}, 
Daniel@0:      case 'dendrogram', i=i+1; show = varargin{i}; 
Daniel@0:      case 'size',       i=i+1; markersize = varargin{i}; 
Daniel@0:      case 'linecolor',  i=i+1; linecolor = varargin{i}; 
Daniel@0:      case 'linewidth',  i=i+1; linewidth = varargin{i};
Daniel@0:      case 'color',      i=i+1; datacolor = varargin{i};
Daniel@0:      case 'coord',      i=i+1; datacoord = varargin{i};
Daniel@0:      case {'on','off'}, show = varargin{i}; 
Daniel@0:      otherwise argok=0; 
Daniel@0:     end
Daniel@0:   elseif isstruct(varargin{i}), datacoord = varargin{i}; 
Daniel@0:   else argok = 0; 
Daniel@0:   end
Daniel@0:   if ~argok, disp(['(som_clplot) Ignoring invalid argument #' num2str(i+1)]); end
Daniel@0:   i=i+1;
Daniel@0: end
Daniel@0: 
Daniel@0: % markersize
Daniel@0: if length(markersize)==1, markersize = ones(2*clen-1,1)*markersize; end
Daniel@0: 
Daniel@0: % datacoord
Daniel@0: if ~isempty(datacoord),
Daniel@0:   if isstruct(datacoord), 
Daniel@0:     switch datacoord.type, 
Daniel@0:      case 'som_map',   datacoord = datacoord.topol;
Daniel@0:      case 'som_topol', %nil 
Daniel@0:      case 'som_data',  datacoord = datacoord.data;
Daniel@0:      otherwise,        datacoord = []; 
Daniel@0:     end  
Daniel@0:   end
Daniel@0:   if isstruct(datacoord), 
Daniel@0:     sC = som_clstruct(sC,'coord',som_vis_coords(datacoord.lattice,datacoord.msize));
Daniel@0:   else
Daniel@0:     [dlen dim] = size(datacoord);
Daniel@0:     if dim>2, datacoord = pcaproj(datacoord,2); end
Daniel@0:     sC = som_clstruct(sC,'coord',datacoord);
Daniel@0:   end
Daniel@0: end
Daniel@0: 
Daniel@0: % show
Daniel@0: if ischar(show), show = strcmp(show,'on'); end
Daniel@0: if prod(size(show)) == 1, show = ones(2*clen-1,1)*show; end
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %% initialize values
Daniel@0: 
Daniel@0: % find the children to show for each cluster
Daniel@0: sTree0 = struct('parent',0,'children',[]); 
Daniel@0: sTree = sTree0; 
Daniel@0: for i=2:(2*clen-1), sTree(i) = sTree0; end
Daniel@0: for i=(clen+1):(2*clen-1), 
Daniel@0:   if isfinite(sC.tree(i-clen,3)), 
Daniel@0:     ch = sC.tree(i-clen,1:2);
Daniel@0:     sTree(i).children = ch; 
Daniel@0:     for j=1:length(ch), sTree(ch(j)).parent = i; end
Daniel@0:   end  
Daniel@0: end
Daniel@0: if any(show==0), % some clusters are not shown
Daniel@0:   for i=(clen+1):(2*clen-1), 
Daniel@0:     if ~show(i),
Daniel@0:       p = sTree(i).parent;
Daniel@0:       ch = sTree(i).children;
Daniel@0:       if p, 
Daniel@0: 	j = find(sTree(p).children == i);
Daniel@0: 	sTree(p).children = [sTree(p).children([1:(j-1),(j+1):end]), ch]; 
Daniel@0: 	for j=1:length(ch), sTree(ch(j)).parent = p; end
Daniel@0:       end
Daniel@0:     end    
Daniel@0:   end  
Daniel@0: end
Daniel@0: 
Daniel@0: % the arcs
Daniel@0: lfrom = []; lto = []; ladd = [];
Daniel@0: for i=(clen+1):(2*clen-1),   
Daniel@0:   if show(i), 
Daniel@0:     ch = sTree(i).children'; 
Daniel@0:     %ch = ch(find(show(ch)==1)); 
Daniel@0:     lfrom = [lfrom; i*ones(length(ch),1)]; 
Daniel@0:     lto = [lto; ch];     
Daniel@0:   end
Daniel@0: end
Daniel@0: 
Daniel@0: % infinite height
Daniel@0: %isinf = ~isfinite(sC.height); 
Daniel@0: %sC.height(isinf) = 2*max(sC.height(~isinf)); 
Daniel@0: 
Daniel@0: % the coordinates of the arcs
Daniel@0: Co = [sC.coord, sC.height];
Daniel@0: if size(Co,2)==2, 
Daniel@0:   Lx = [Co(lfrom,1),   Co(lto,1),     Co(lto,1)];
Daniel@0:   Ly = [Co(lfrom,end), Co(lfrom,end), Co(lto,end)];
Daniel@0:   Lz = []; 
Daniel@0: else
Daniel@0:   Lx = [Co(lfrom,1),   Co(lto,1),     Co(lto,1)];
Daniel@0:   Ly = [Co(lfrom,2),   Co(lto,2),     Co(lto,2)];
Daniel@0:   Lz = [Co(lfrom,end), Co(lfrom,end), Co(lto,end)];
Daniel@0: end
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: %% plot
Daniel@0: 
Daniel@0: washold = ishold; 
Daniel@0: if ~washold, cla; hold on; end
Daniel@0: 
Daniel@0: % plot data
Daniel@0: if ~isempty(datacoord), 
Daniel@0:   if isempty(datacolor),
Daniel@0:     nancolor = get(gcf,'Color'); 
Daniel@0:     Col = nancolor(ones(length(sC.base),1),:);
Daniel@0:     ind = find(isfinite(sC.base)); 
Daniel@0:     Col(ind,:) = sC.color(sC.base(ind),:); 
Daniel@0:   elseif size(datacolor,2)==1, Col = som_normcolor(datacolor,jet); 
Daniel@0:   else Col = datacolor;     
Daniel@0:   end    
Daniel@0:   if isstruct(datacoord), som_cplane(datacoord,Col);
Daniel@0:   else som_grid('rect',[length(sC.base) 1],'line','none',...
Daniel@0: 		'Coord',datacoord,'Markercolor',Col); 
Daniel@0:   end
Daniel@0: end
Daniel@0: 
Daniel@0: h = []; 
Daniel@0: if any(show), 
Daniel@0: 
Daniel@0:   % plot the lines
Daniel@0:   if isempty(Lz), 
Daniel@0:     h = line(Lx',Ly','color',linecolor,'linewidth',linewidth); 
Daniel@0:   else 
Daniel@0:     h = line(Lx',Ly',Lz','color',linecolor,'linewidth',linewidth); 
Daniel@0:     if ~washold, view(3); end
Daniel@0:     rotate3d on
Daniel@0:   end
Daniel@0:   
Daniel@0:   % plot the nodes
Daniel@0:   inds = find(show); 
Daniel@0:   som_grid('rect',[length(inds) 1],'line','none',...
Daniel@0: 	   'Coord',Co(inds,:),...
Daniel@0: 	   'Markercolor',sC.color(inds,:),...
Daniel@0: 	   'Markersize',markersize(inds));
Daniel@0: end
Daniel@0: 
Daniel@0: if ~washold, hold off, end
Daniel@0: 
Daniel@0: return;
Daniel@0: 
Daniel@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Daniel@0: 
Daniel@0: 
Daniel@0: 
Daniel@0: