63 lines
2.2 KiB
Mathematica
63 lines
2.2 KiB
Mathematica
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function [cm lab dist] = getmatrix(tr,varargin)
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%GETMATRIX converts a Phytree Object into a relationship matrix.
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%
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% [MATRIX, ID, DISTANCES] = GETMATRIX(T) converts the phylogenetic tree
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% object T into a logical sparse matrix, where 1's indicate that a branch
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% node (row index) is connected to its child (column index). The child
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% can be either another branch node or a leaf node. ID is a list of the
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% labels that correspond to the rows and columns of MATRIX, first the
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% leaf nodes from 1 to NUMLEAVES, then the branch nodes from NUMLEAVES+1
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% to NUMLEAVES+NUMBRANCHES, being the root the last node. DISTANCES is
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% a column vector with one entry for every nonzero entry in MATRIX
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% traversed columnwise and representing the distance between the branch
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% node and the child.
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%
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% Example:
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%
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% T = phytreeread('pf00002.tree')
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% [MATRIX ID DIST] = getmatrix(T);
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%
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% See also PHYTREE, PHYTREE/GET, PHYTREE/PDIST, PHYTREE/PRUNE, PHYTREETOOL.
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% Copyright 2006 The MathWorks, Inc.
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% $Revision: 1.1.6.1 $ $Date: 2006/06/16 20:06:43 $
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%%% check arguments
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if nargin > 1
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if rem(nargin,2) == 0
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error('Bioinfo:phytree:getmatrix:IncorrectNumberOfArguments',...
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'Incorrect number of arguments to %s.',mfilename);
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end
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okargs = {'no_input_arguments'};
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for j=1:2:nargin-2
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pname = varargin{j};
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pval = varargin{j+1};
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if(isstruct(pval))
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error('Bioinfo:phytree:getmatrix:StructParamError',...
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'parameter cannot be a struct');
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end
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k = find(strncmpi(pname, okargs,length(pname)));
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if isempty(k)
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error('Bioinfo:phytree:getmatrix:UnknownParameterName',...
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'Unknown parameter name: %s.',pname);
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elseif length(k)>1
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error('Bioinfo:phytree:getmatrix:AmbiguousParameterName',...
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'Ambiguous parameter name: %s.',pname);
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else
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switch(k)
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end
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end
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end
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end
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numLeaves = size(tr.tree,1)+1;
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numNodes = numLeaves + numLeaves -1;
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cm = sparse(repmat(numLeaves+1:numNodes,1,2),tr.tree(:),true,numNodes,numNodes);
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if nargout>1
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lab = tr.names;
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end
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if nargout>2
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dist = tr.dist;
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end
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