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
235
matlab/graph/@phyTree/phyTree.m
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235
matlab/graph/@phyTree/phyTree.m
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function tr = phyTree(varargin)
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%PHYTREE Phylogenetic tree object.
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%
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% TREE = PHYTREE(B) creates an ultrametric phylogenetic tree object. B is
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% a numeric array of size [NUMBRANCHES X 2] in which every row represents
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% a branch of the tree and it contains two pointers to the branches
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% or leaves nodes which are its children. Leaf nodes are numbered from 1
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% to NUMLEAVES and branch nodes are numbered from NUMLEAVES + 1 to
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% NUMLEAVES + NUMBRANCHES. Note that since only binary trees are allowed,
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% then NUMLEAVES = NUMBRANCHES + 1. Branches are defined in chronological
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% order, i.e. B(i,:) > NUMLEAVES + i. As a consequence, the first row can
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% only have pointers to leaves and the last row must represent the 'root'
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% branch. Parent-child distances are set to the unit or by the ultrametric
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% condition if child is a leaf.
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%
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% TREE = PHYTREE(B,D) creates an additive phylogenetic tree object with
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% branch distances defined by D. D is a numeric array of size [NUMNODES X
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% 1] with the distances of every child node (leaf or branch) to its parent
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% branch. NUMNODES = NUMLEAVES + NUMBRANCHES. D(end), the distance
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% associated to the root node, is meaningless.
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%
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% TREE = PHYTREE(B,C) creates an ultrametric phylogenetic tree object with
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% branch distances defined by C. C is a numeric array of size [NUMBRANCHES
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% X 1] with the coordinates of every branch node. In ultrametric tress all
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% the leaves are at the same location (i.e. same distance to the root).
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%
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% TREE = PHYTREE(BC) creates an ultrametric phylogenetic binary tree
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% object with branch pointers in BC(:,[1 2]) and branch coordinates in
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% BC(:,3). Same as PHYTREE(B,C).
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%
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% TREE = PHYTREE(...,N) specifies the names for the leaves and/or the
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% branches. N is a cell of strings. If NUMEL(N)==NUMLEAVES then the names
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% are assigned chronologically to the leaves. If NUMEL(N)==NUMBRANCHES the
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% names are assigned to the branch nodes. If NUMEL(N)==NUMLEAVES +
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% NUMBRANCHES all the nodes are named. Unassigned names default to 'Leaf
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% #' and/or 'Branch #' as required.
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%
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% TREE = PHYTREE creates an empty phylogenectic tree object
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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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% b = [1 2; 3 4; 5 6; 7 8;9 10];
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% t = phytree(b);
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% view(t)
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%
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% % create an ultrametric tree with specified branch distances
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% bd = [.1 .2 .3 .3 .4 ]';
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% b = [1 2; 3 4; 5 6; 7 8;9 10];
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% t = phytree(b,bd);
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% view(t)
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%
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% See also PHYTREE/GET, PHYTREE/SELECT, PHYTREEREAD, PHYTREETOOL,
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% PHYTREEWRITE, SEQLINKAGE, SEQNEIGHJOIN, SEQPDIST.
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% Copyright 2003-2006 The MathWorks, Inc.
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% $Revision: 1.1.6.11.2.1 $ $Author: batserve $ $Date: 2006/07/27 21:37:49 $
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justVerifyValidity = false;
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switch nargin
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case 0
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tr.tree = zeros(0,2);
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tr.dist = zeros(0,1);
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tr.names = {};
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case 1
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B = varargin{1};
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case 2
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B = varargin{1};
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if iscell(varargin{2})
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N = varargin{2};
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else
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D = varargin{2};
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end
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case 3
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B = varargin{1};
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D = varargin{2};
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N = varargin{3};
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otherwise
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error('Bioinfo:phytree:IncorrectNumberOfArguments',...
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'Incorrect number of arguments to %s.',mfilename);
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end
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if nargin==1 && isstruct(B) && isfield(B,'tree') && isfield(B,'names') && isfield(B,'dist')
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N = B.names;
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D = B.dist;
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B = B.tree;
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tr.tree = B;
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tr.dist = D;
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tr.names = N;
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justVerifyValidity = true;
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end
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if nargin
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if isnumeric(B)
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switch size(B,2)
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case 2
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% ok
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case 3
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D = B(:,3);
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B(:,3)=[];
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otherwise
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error('Bioinfo:phytree:IncorrectSize','Incorrect size for B or BC')
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end
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else
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error('Bioinfo:phytree:IncorrectType','Incorrect type for B or BC')
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end
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% test B
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if sum(diff(sort(B(:)))~=1) || (min(B(:))~=1)
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error('Bioinfo:phytree:IncompleteTree','Branch architecture is not complete')
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end
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numBranches = size(B,1);
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numLeaves = numBranches + 1;
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numLabels = numBranches + numLeaves;
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h=all(B'>=repmat(numLeaves+1:numLabels,2,1));
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if any(h)
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error('Bioinfo:phytree:NonChronologicalTree',...
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['Branch(es) not in chronological order: [' num2str(find(h)) ']'])
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end
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if exist('D','var')
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if ~isnumeric(D) || any(D(:)<0) || ~all(isreal(D)) || size(D,2)~=1
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error('Bioinfo:phytree:DistancesNotValid',...
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'Distances must be a column vector of real positive numbers')
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end
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switch size(D,1)
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case numBranches
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D = [zeros(numLeaves,1); D]; % add ultrametric distances of leaves
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D(B) = D((numLeaves+(1:numBranches))'*[1 1])-D(B); %dist of edges
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D(end) = 0; % set root at zero
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case numLabels
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% ok
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otherwise
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error('Bioinfo:phytree:DistancesNotValid',...
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'Distances must agree either with the number of branches (C) or total nodes (D)')
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end
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else % set defaut D
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% look for parents
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P = zeros(numLabels,1);
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P(B) = repmat((1:numBranches)',1,2);
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P(end) = numBranches;
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% look at which level is every branch
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L = zeros(numLabels,1);
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for ind = 1:numBranches
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L(ind+numLeaves) = max(L(B(ind,:))+1);
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end
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D = L(P+numLeaves)-L;
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end
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% set default names
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for ind = 1:numLeaves
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names{ind}=['Leaf ' num2str(ind)]; %#ok
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end
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for ind = 1:numBranches
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names{ind+numLeaves}=['Branch ' num2str(ind)];
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end
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if exist('N','var')
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if ~iscell(N)
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error('Bioinfo:phytree:NamesNotValid',...
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'Names must be supplied with a cell of strings')
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end
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switch numel(N)
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case numLabels
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h = 1:numLabels;
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case numLeaves
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h = 1:numLeaves;
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case numBranches
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h = numLeaves+1:numLabels;
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otherwise
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error('Bioinfo:phytree:NamesNotValid',...
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'Names must agree either with the number of branches, number of leaves, or total nodes')
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end
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for ind = 1:length(h);
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str = N{ind};
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if ~ischar(str)
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error('Bioinfo:phytree:NamesNotValid',...
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'Names must be valid strings')
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end
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names{h(ind)}=str;
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end
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% check that none of the names is empty
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for ind = 1:numLabels
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if isempty(names{ind})
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if ind > numLeaves
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names{ind} = ['Branch ' num2str(ind-numLeaves)];
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else
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names{ind} = ['Leaf ' num2str(ind)];
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end
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end
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end
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if numel(unique(names))~=numLabels
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error('Bioinfo:phytree:NamesNotUnique',...
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'Names for leaves and branches must be unique')
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end
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end
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% check and corrects a non-monotonic tree
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monotonicWarning = false;
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for ind = 1:numBranches
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if any(D(B(ind,:))<0)
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monotonicWarning = true;
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tmp = min(D(B(ind,:)));
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D(B(ind,:)) = D(B(ind,:)) - tmp;
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D(numLeaves+ind) = D(numLeaves+ind) + tmp;
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end
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end
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if monotonicWarning
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warning('Bioinfo:phytree:NonMonotonicTree',...
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'Non consistent branch distances; \n Incremented branch lengths to hold a Monotonic Phylogenetic Tree')
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end
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if justVerifyValidity
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tr = class(tr,'phytree');
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return
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end
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tr.tree = B;
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tr.dist = D;
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tr.names = names(:);
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% reorder such that there will be no crossings in the displayed tree
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tr = prettyOrder(tr);
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end %if nargin
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% for trees of only one branch correct dimensions
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% if size(tr.tree,2) <2 tr.tree = tr.tree'; end
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% Makes the tree a class
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tr = class(tr,'phyTree');
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