Added source Matlab code for reference

matlab/graph/@phyTree/Subtree.m

@@ -0,0 +1,91 @@
+function subtr = subtree(tr,nodes)
+%SUBTREE Extracts a subtree.
+%
+%   T2 = SUBTREE(T1,NODES) Extracts a new subtree T2 in which the new root
+%   is the first common ancestor of the NODES vector from T1. NODES in the
+%   tree are indexed as [1:NUMLEAVES] for the leaves and as [NUMLEAVES+1 :
+%   NUMLEAVES+NUMBRANCHES] for the branches. NODES can also be a logical
+%   array of following sizes: [NUMLEAVES+NUMBRANCHES x 1], [NUMLEAVES x 1]
+%   or [NUMBRANCHES x 1]. 
+%
+%   Example:
+%
+%      % Load a phylogenetic tree created from a protein family:
+%      tr = phytreeread('pf00002.tree')
+%       
+%      % Get the subtree that contains the VIPS and CGRR human proteins:
+%      sel = getbyname(tr,{'vips_human','cgrr_human'});
+%      sel = any(sel,2);
+%      tr =  subtree(tr,sel)
+%      view(tr);
+%       
+%   See also PHYTREE, PHYTREE/PRUNE, PHYTREE/SELECT, PHYTREE/GET,
+%   PHYTREE/GETBYNAME. 
+
+% Copyright 2003-2005 The MathWorks, Inc.
+% $Revision: 1.1.8.1 $ $Author: batserve $ $Date: 2005/06/09 21:57:04 $
+
+if numel(tr)~=1
+     error('Bioinfo:phytree:subtree:NoMultielementArrays',...
+           'Phylogenetic tree must be an 1-by-1 object.');
+end
+numBranches = size(tr.tree,1);
+numLeaves = numBranches + 1;
+numLabels = numBranches + numLeaves; 
+
+% validate nodes
+if islogical(nodes)
+    if numel(nodes)==numLabels 
+        nodes = nodes(:)==true;
+    elseif numel(nodes)==numLeaves
+        nodes = [nodes(:);false(numBranches,1)];
+    elseif numel(nodes)==numBranches
+        nodes = [false(numLeaves,1);nodes(:)];
+    else
+        error('Bioinfo:phytree:subtree:IncorrectSizeInputVector',...
+              'Logical vector must have the same number of elements as nodes in the Phylogenetic Tree.');
+    end
+elseif isnumeric(nodes) && isreal(nodes) && all(nodes(:)>=1) && all(nodes(:)<=numLabels)
+    tem = false(numLabels,1);
+    tem(floor(nodes(:))) = true;
+    nodes=tem(:);
+else
+    error('Bioinfo:phytree:subtree:InvalidInputNodes',...
+          'Invalid value for NODES.');
+end
+
+% at this point NODES should only be a logical vector
+
+if (~any(nodes(numLeaves+1:numLabels)) && (sum(nodes(1:numLeaves))<2))
+    error('Bioinfo:phytree:subtree:InvalidSubtree',...
+          'Subtree must contain at least two leaves.');
+end
+
+
+% look for the first common ancestor that contains all selected nodes,
+% accumulating the selected nodes towards the root, the common ancestor
+% will be the first sum equal to the number of selected nodes
+branchWidth = double(nodes);
+for ind = 1:numBranches
+    branchWidth(numLeaves+ind) = branchWidth(numLeaves+ind) + ...
+                                 sum(branchWidth(tr.tree(ind,:)));
+end
+commonAncestor = find(branchWidth==sum(nodes),1);
+
+% now propagate the ancestor new) root towards the leaves to find all the
+% nodes that should stay for the subtree
+sel = false(1,numLabels);
+sel(commonAncestor) = true;
+for ind = commonAncestor:-1:numLeaves+1
+    sel(tr.tree(ind-numLeaves,:)) = sel(ind);
+end
+    
+% extract the subtree
+permuta = find(sel);
+subtr=phytree;
+ipermuta(permuta) = 1:length(permuta);
+subtrNumLeaves = (ipermuta(end) + 1)/2;
+subtr.tree = ipermuta(tr.tree(permuta(subtrNumLeaves+1:end)-numLeaves,:));
+subtr.dist = tr.dist(permuta);
+subtr.names = tr.names(permuta);
+subtr.dist(end) = 0;