comparison toolboxes/MIRtoolbox1.3.2/somtoolbox/som_dendrogram.m @ 0:e9a9cd732c1e tip

first hg version after svn

+function [h,Coord,Color,height] = som_dendrogram(Z,varargin)
+
+%SOM_DENDROGRAM Visualize a dendrogram.
+%
+% [h,Coord,Color,height] = som_dendrogram(Z, [[argID,] value, ...])
+%
+%  Z = som_linkage(sM); 
+%  som_dendrogram(Z); 
+%  som_dendrogram(Z,sM); 
+%  som_dendrogram(Z,'coord',co); 
+%
+%  Input and output arguments ([]'s are optional):
+%   h        (vector) handle to the arc lines
+%   Z        (matrix) size n-1 x 1, the hierarchical cluster matrix
+%                     returned by functions like LINKAGE and SOM_LINKAGE
+%                     n is the number of original data samples.
+%   [argID,  (string) See below. The values which are unambiguous can 
+%    value]  (varies) be given without the preceeding argID.
+%   Coord    (matrix) size 2*n-1 x {1,2}, the coordinates of the
+%                     original data samples and cluster nodes used 
+%                     in the visualization
+%   Color    (matrix) size 2*n-1 x 3, the colors of ...
+%   height   (vector) size 2*n-1 x 1, the heights of ...
+%   
+% Here are the valid argument IDs and corresponding values. The values 
+% which are unambiguous (marked with '*') can be given without the
+% preceeding argID.
+%   'data'  *(struct) map or data struct: many other optional 
+%                     arguments require this 
+%            (matrix) data matrix
+%   'coord'  (matrix) size n x 1 or n x 2, the coordinates of 
+%                     the original data samples either in 1D or 2D
+%            (matrix) size 2*n-1 x {1,2}, the coordinates of both
+%                     original data samples and each cluster
+%           *(string) 'SOM', 'pca#', 'sammon#', or 'cca#': the coordinates
+%                     are calculated using the given data and the 
+%                     required projection algorithm. The '#' at the
+%                     end of projection algorithms refers to the 
+%                     desired output dimension and can be either 1 or 2
+%                     (2 by default). In case of 'SOM', the unit
+%                     coordinates (given by SOM_VIS_COORDS) are used.
+%   'color'  (matrix) size n x 3, the color of the original data samples
+%            (matrix) size 2*n-1 x 3, the colors of both original 
+%                     data samples and each cluster
+%            (string) color specification, e.g. 'r.', used for each node
+%   'height' (vector) size n-1 x 1, the heights used for each cluster
+%            (vector) size 2*n-1 x 1, the heights used for both original
+%                     data samples and each cluster
+%           *(string) 'order', the order of combination determines height
+%                     'depth', the depth at which the combination
+%                     happens determines height
+%   'linecolor' (string) color specification for the arc color, 'k' by default
+%               (vector) size 1 x 3
+%
+% See also SOM_LINKAGE, DENDROGRAM.
+
+% Copyright (c) 2000 by Juha Vesanto
+% Contributed to SOM Toolbox on June 16th, 2000 by Juha Vesanto
+% http://www.cis.hut.fi/projects/somtoolbox/
+ 
+% Version 2.0beta juuso 160600
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% read the arguments
+
+% Z 
+nd = size(Z,1)+1; 
+nc = size(Z,1); 
+
+% varargin
+Coordtype = 'natural'; Coord = []; codim = 1; 
+Colortype = 'none'; Color = [];
+height = [zeros(nd,1); Z(:,3)]; 
+M = []; 
+linecol = 'k'; 
+
+i=1; 
+while i<=length(varargin), 
+  argok = 1; 
+  if ischar(varargin{i}), 
+    switch varargin{i}, 
+     case 'data', i = i + 1; M = varargin{i}; 
+     case 'coord', 
+      i=i+1; 
+      if isnumeric(varargin{i}), Coord = varargin{i}; Coordtype = 'given'; 
+      else 
+	if strcmp(varargin{i},'SOM'), Coordtype = 'SOM'; 
+	else Coordtype = 'projection'; Coord = varargin{i}; 
+	end
+      end
+     case 'color', 
+      i=i+1; 
+      if isempty(varargin{i}), Colortype = 'none'; 
+      elseif ischar(varargin{i}), Colortype = 'colorspec'; Color = varargin{i};
+      else Colortype = 'given'; Color = varargin{i}; 
+      end
+     case 'height', i=i+1; height = varargin{i}; 
+     case 'linecolor', i=i+1; linecol = varargin{i}; 
+     case 'SOM', 
+      Coordtype = 'SOM'; 
+     case {'pca','pca1','pca2','sammon','sammon1','sammon2','cca','cca1','cca2'}, 
+      Coordtype = 'projection'; Coord = varargin{i}; 
+     case {'order','depth'}, height = varargin{i};  
+    end
+  elseif isstruct(varargin{i}), M = varargin{i}; 
+  else
+    argok = 0; 
+  end
+  if ~argok, 
+    disp(['(som_dendrogram) Ignoring invalid argument #' num2str(i+1)]); 
+  end
+  i = i+1; 
+end
+
+switch Coordtype, 
+ case 'SOM', 
+  if isempty(M) | ~any(strcmp(M.type,{'som_map','som_topol'})) , 
+    error('Cannot determine SOM coordinates without a SOM.'); 
+  end
+  if strcmp(M.type,'som_map'), M = M.topol; end
+ case 'projection', 
+  if isempty(M), error('Cannot do projection without the data.'); end
+  if isstruct(M), 
+    if strcmp(M.type,'som_data'), M = M.data; 
+    elseif strcmp(M.type,'som_map'), M = M.codebook; 
+    end
+  end  
+  if size(M,1) ~= nd, 
+    error('Given data must be equal in length to the number of original data samples.')
+  end    
+ case 'given', 
+  if size(Coord,1) ~= nd & size(Coord,1) ~= nd+nc, 
+    error('Size of given coordinate matrix does not match the cluster hierarchy.');
+  end  
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% initialization
+
+% Coordinates
+switch Coordtype, 
+ case 'natural', o = leavesorder(Z)'; [dummy,Coord] = sort(o); codim = 1; 
+ case 'SOM', Coord = som_vis_coords(M.lattice,M.msize); codim = 2;   
+ case 'projection', 
+  switch Coord, 
+   case {'pca','pca2'},       Coord = pcaproj(M,2);   codim = 2; 
+   case 'pca1',               Coord = pcaproj(M,1);   codim = 1; 
+   case {'cca','cca2'},       Coord = cca(M,2,20);    codim = 2; 
+   case 'cca1',               Coord = cca(M,1,20);    codim = 1; 
+   case {'sammon','sammon2'}, Coord = sammon(M,2,50); codim = 2; 
+   case 'sammon1',            Coord = sammon(M,1,50); codim = 1; 
+  end
+ case 'given', codim = min(size(Coord,2),2); % nill
+end
+
+if size(Coord,1) == nd, 
+  Coord = [Coord; zeros(nc,size(Coord,2))]; 
+  for i=(nd+1):(nd+nc), 
+    leaves = leafnodes(Z,i,nd);
+    if any(leaves), Coord(i,:) = mean(Coord(leaves,:),1); else Coord(i,:) = Inf; end
+  end
+end
+
+% Colors
+switch Colortype, 
+ case 'colorspec', % nill
+ case 'none', Color = ''; 
+ case 'given',
+  if size(Color,1) == nd, 
+    Color = [Color; zeros(nc,3)]; 
+    for i=(nd+1):(nd+nc), 
+      leaves = leafnodes(Z,i,nd);
+      if any(leaves), Color(i,:) = mean(Color(leaves,:),1); 
+      else Color(i,:) = 0.8; 
+      end
+    end
+  end
+end
+
+% height
+if ischar(height), 
+  switch height, 
+   case 'order', height = [zeros(nd,1); [1:nc]']; 
+   case 'depth', height = nodedepth(Z); height = max(height) - height; 
+  end
+else
+  if length(height)==nc, height = [zeros(nd,1); height]; end
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% draw
+
+% the arcs
+lfrom = []; lto = []; 
+for i=1:nd+nc, 
+  if i<=nd, ch = [];  
+  elseif ~isfinite(Z(i-nd,3)), ch = []; 
+  else ch = Z(i-nd,1:2)'; 
+  end
+  if any(ch), 
+    lfrom = [lfrom; i*ones(length(ch),1)]; 
+    lto = [lto; ch]; 
+  end
+end
+
+% the coordinates of the arcs
+if codim == 1, 
+  Lx = [Coord(lfrom), Coord(lto), Coord(lto)];
+  Ly = [height(lfrom), height(lfrom), height(lto)];
+  Lz = []; 
+else
+  Lx = [Coord(lfrom,1), Coord(lto,1), Coord(lto,1)];
+  Ly = [Coord(lfrom,2), Coord(lto,2), Coord(lto,2)];
+  Lz = [height(lfrom), height(lfrom), height(lto)];
+end
+
+washold = ishold; 
+if ~washold, cla; end
+
+% plot the lines
+if isempty(Lz), 
+  h = line(Lx',Ly','color',linecol); 
+else 
+  h = line(Lx',Ly',Lz','color',linecol); 
+  if ~washold, view(3); end
+  rotate3d on
+end
+
+% plot the nodes
+hold on
+switch Colortype, 
+ case 'none', % nill
+ case 'colorspec', 
+  if codim == 1, plot(Coord,height,Color); 
+  else plot3(Coord(:,1), Coord(:,2), height, Color); 
+  end
+ case 'given', 
+  som_grid('rect',[nd+nc 1],'line','none','Coord',[Coord, height],...
+	   'Markersize',10,'Markercolor',Color);
+end
+if ~washold, hold off, end
+
+return;
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% subfunctions
+
+function depth = nodedepth(Z)
+
+  nd = size(Z,1)+1; 
+  nc = size(Z,1);  
+  depth = zeros(nd+nc,1); 
+  ch = nc+nd-1; 
+  while any(ch), 
+    c  = ch(1); ch = ch(2:end);
+    if c>nd & isfinite(Z(c-nd,3)), 
+      chc = Z(c-nd,1:2); 
+      depth(chc) = depth(c) + 1; 
+      ch = [ch, chc]; 
+    end
+  end
+  return;
+
+function inds = leafnodes(Z,i,nd)
+
+  inds = []; 
+  ch = i; 
+  while any(ch), 
+    c  = ch(1); ch = ch(2:end);
+    if c>nd & isfinite(Z(c-nd,3)), ch = [ch, Z(c-nd,1:2)]; end
+    if c<=nd, inds(end+1) = c; end 
+  end
+  return;
+
+function order = leavesorder(Z)
+
+  nd = size(Z,1)+1;
+  order = 2*nd-1; 
+  nonleaves = 1; 
+  while any(nonleaves), 
+    j = nonleaves(1); 
+    ch = Z(order(j)-nd,1:2);
+    if j==1, oleft = []; else oleft = order(1:(j-1)); end
+    if j==length(order), oright = []; else oright = order((j+1):length(order)); end
+    order = [oleft, ch, oright];
+    nonleaves = find(order>nd); 
+  end
+  return; 
+
+
+