40 lines
1.4 KiB
Mathematica
40 lines
1.4 KiB
Mathematica
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function tr = prettyOrder(tr)
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%PRETTYORDER Reorders the leaf nodes to avoid branch crossings.
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%
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% T2 = PRETTYORDER(T1) Reorders the leaf nodes in the phylogenetic tree
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% T1 such that the layout of the tree does not contain branch crossings.
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% Copyright 2003-2005 The MathWorks, Inc.
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% $Revision: 1.1.8.1 $ $Author: batserve $ $Date: 2005/06/09 21:56:11 $
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numBranches = size(tr.tree,1);
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numLeaves = numBranches + 1;
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numLabels = numBranches + numLeaves;
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L = [ones(numLeaves,1); zeros(numBranches,1)];
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for ind = 1 : numBranches
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L(ind+numLeaves) = sum(L(tr.tree(ind,:)));
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end
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X = zeros(numLabels,1);
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for ind = numBranches:-1:1
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X(tr.tree(ind,:)) = tr.dist(tr.tree(ind,:))+X(ind+numLeaves);
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end
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Li = zeros(1,numLabels); Ls = Li;
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Ls(numLabels) = numLeaves;
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for ind = numBranches:-1:1
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Ls(tr.tree(ind,:)) = Ls(ind+numLeaves);
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Li(tr.tree(ind,:)) = Li(ind+numLeaves);
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if diff(X(tr.tree(ind,:)))>=0
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Ls(tr.tree(ind,1)) = Li(tr.tree(ind,1)) + L(tr.tree(ind,1));
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Li(tr.tree(ind,2)) = Ls(tr.tree(ind,2)) - L(tr.tree(ind,2));
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else
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Ls(tr.tree(ind,2)) = Li(tr.tree(ind,2)) + L(tr.tree(ind,2));
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Li(tr.tree(ind,1)) = Ls(tr.tree(ind,1)) - L(tr.tree(ind,1));
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end
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end
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tr.names(Ls(1:numLeaves))=tr.names(1:numLeaves);
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tr.dist(Ls(1:numLeaves))=tr.dist(1:numLeaves);
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Ls(numLeaves+1:numLabels)=numLeaves+1:numLabels;
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tr.tree = Ls(tr.tree);
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