Added source Matlab code for reference
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Waldir Leoncio
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186 changed files with 61405 additions and 1 deletions
206
matlab/graph/@phyTree/reRoot.m
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206
matlab/graph/@phyTree/reRoot.m
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function tr = reRoot(tr,node,distance)
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%REROOT changes the root of a phylogenetic tree.
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%
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% T2 = REROOT(T1) changes the root of the phylogenetic tree T1 using the
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% mid-point method. The mid-point is the location where the means of
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% the branch lengths of either side of the tree are equalized. The
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% original root is deleted.
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%
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% T2 = REROOT(T1,NODE) changes the root to the branch indexed by NODE.
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% The new root is placed at half the distance between NODE and its
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% parent.
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%
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% T2 = REROOT(T1,NODE,DISTANCE) re-roots T1 by placing the new root at a
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% given DISTANCE from the reference NODE towards the root of the tree.
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%
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% Note: The new branch in T2 representing the root is labeled as 'Root'.
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%
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% Example:
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%
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% % Create an ultrametric tree
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% tr_1 = phytree([5 7;8 9;6 11; 1 2;3 4;10 12;14 16;15 17;13 18])
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% plot(tr_1,'branchlabels',true)
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%
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% % Place the new root at 'Branch 7'
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% sel = getbyname(tr_1,'Branch 7');
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% tr_2 = reroot(tr_1,sel)
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% plot(tr_2,'branchlabels',true)
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%
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% % The mid-point of the original tree was the root, since it was an
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% % ultrametric tree
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% tr_3 = reroot(tr_2)
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% plot(tr_3,'branchlabels',true)
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%
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% See also PHYTREE, PHYTREE/GET, PHYTREE/GETBYNAME, PHYTREE/PRUNE,
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% PHYTREE/SELECT, SEQNEIGHJOIN.
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% Copyright 2003-2006 The MathWorks, Inc.
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% $Revision: 1.1.8.3 $ $Author: batserve $ $Date: 2006/06/16 20:06:46 $
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if numel(tr)~=1
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error('Bioinfo:phytree:reroot:NoMultielementArrays',...
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'Phylogenetic tree must be an 1-by-1 object.');
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end
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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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if nargin == 1;
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[node,distance] = midpoint(tr);
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else
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% validate node
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if islogical(node)
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if any(numel(node) == [numLabels numLeaves])
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node = find(node);
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elseif numel(node) == numBranches
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node = find(node) + numLeaves;
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else
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error('Bioinfo:phytree:reroot:IncorrectSizeInputVector',...
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'Logical vector must have the same number of elements as nodes in the Phylogenetic Tree.');
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end
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end
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if ~isscalar(node) || node<1 || node>numLabels
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error('Bioinfo:phytree:reroot:InvalidInputNode',...
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'Invalid value for NODE.');
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end
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node = round(node);
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% when no distance is given put the root at half the branch
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if nargin<3
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distance = tr.dist(node)/2;
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end
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end
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% find parents for every tree node
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parent = zeros(numLabels,1);
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parent(tr.tree) = repmat(numLeaves+1:numLabels,1,2);
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% validate distance, if necessary shift the origin node
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if ~isscalar(distance) || distance<0
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error('Bioinfo:phytree:reroot:InvalidInputDistance',...
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'Invalid value for DISTANCE.');
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end
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% validate distance, if necessary shift the origin node
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while (tr.dist(node)<=distance) && (node ~= numLabels)
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distance = distance - tr.dist(node);
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node = parent(node);
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end
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if node == numLabels
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if distance>0
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warning('Bioinfo:phytree:reroot:BeyondRoot',...
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'Distance goes beyond the root, tree unchanged.')
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else
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tr.names{end} = 'Root';
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end
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return
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end
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% check if we just need to move the branches of current root
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if parent(node) == numLabels
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tr.dist(setxor(tr.tree(end,:),node)) = ...
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sum(tr.dist(tr.tree(end,:))) - distance;
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tr.dist(node) = distance;
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tr.names{end} = 'Root';
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return
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end
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% path to root from node and bros for every point in the path
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path2r = false(numBranches,1);
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pathBros = [];
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me = node;
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par = parent(node);
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while par
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pathBros = [pathBros;setxor(tr.tree(par-numLeaves,:),me)];
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path2r(par-numLeaves) = true;
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me = par;
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par = parent(par);
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end
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path2rInd=find(path2r)+numLeaves;
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% new tree pointers
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tr.tree = [tr.tree(~path2r,:);...
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[[pathBros(end-1:-1:1);node],[pathBros(end);path2rInd(end-1:-1:1)]]];
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% swapping distances in the nodes that belong to the path2r
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tr.dist(pathBros(end)) = tr.dist(pathBros(end)) + tr.dist(path2rInd(end-1));
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tr.dist(path2rInd(2:end-1)) = tr.dist(path2rInd(1:end-2));
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tr.dist(parent(node)) = tr.dist(node) - distance;
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tr.dist(node) = distance;
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% some branches changed positions, need to tree
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permuta = [(1:numLeaves)';find(~path2r)+numLeaves;...
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path2rInd(end-1:-1:1);numLabels];
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ipermuta(permuta)=1:numLabels;
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tr.tree = ipermuta(tr.tree);
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tr.dist = tr.dist(permuta);
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tr.names = tr.names(permuta);
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tr.names{end} = 'Root';
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% re-order leaves for no branch crossings
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tr = prettyorder(tr);
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%-% ----------------------------------------------------------------
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% Selects the point where the mean of the branch length is equalized
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function [node,distance] = midpoint(tr)
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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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branchWidth = ones(numLabels,1);
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downDist = zeros(numLabels,1);
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upDist = zeros(numLabels,1);
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% cumulative distance and width downwards the tree
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for ind = 1:numBranches
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branchWidth(numLeaves+ind) = sum(branchWidth(tr.tree(ind,:)));
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downDist(numLeaves+ind) = sum(downDist(tr.tree(ind,:)) + ...
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tr.dist(tr.tree(ind,:)).*branchWidth(tr.tree(ind,:)));
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end
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% backpropagate distances
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for ind = numBranches:-1:1
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upDist(tr.tree(ind,:)) = downDist(tr.tree(ind,[2 1])) +...
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upDist(ind+numLeaves) + ...
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tr.dist(ind+numLeaves).*(numLeaves-branchWidth(ind+numLeaves)) + ...
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tr.dist(tr.tree(ind,[2 1])).*(branchWidth(tr.tree(ind,[2 1])));
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end
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% find all possible midpoints, solve this eq for every edge
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% ud/Nu + (x)*e = dd/Nd + (1-x)*e
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% ud = cumulative upwards distances
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% dd = cumulative downwards distances
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% Nu = number of leaves in the upper braches
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% Nd = number of leaves in the lower braches
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% e = distance of current edge
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h = tr.dist~=0; % root can not be in an edge which length is zero
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h(numLabels) = false; % the route can not be segmented
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x = inf(numLabels,1);
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x(h) = (upDist(h)./branchWidth(h) - ...
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downDist(h)./(numLeaves-branchWidth(h)))./tr.dist(h)/2 + 1/2;
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x(h) = (upDist(h)./(numLeaves-branchWidth(h)) - ...
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downDist(h)./(branchWidth(h)))./tr.dist(h)/2 + 1/2;
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% find all possible roots
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h = find(x>=0 & x<=1);
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if isempty(h)
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[dummy,h] = min(abs(x-1/2)); %#ok
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end
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% pick the most balanced one
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[d,g]=min(abs(branchWidth(h)*2-numLeaves)); %#ok
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node = h(g);
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ratio = min(max(x(h(g)),0),1);
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% if ratio is 1 then better pick the parent
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if ratio == 1
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[node,dummy] = find(tr.tree==node); %#ok
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node = node + numLeaves;
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ratio = 0;
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end
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% change the ratio (x) to the distance to the selected node
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distance = ratio .* tr.dist(node);
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