630 lines
25 KiB
Mathematica
630 lines
25 KiB
Mathematica
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function handles = Plot(tr,varargin)
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%PLOT renders a phylogenetic tree.
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%
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% PLOT(TREE) renders a phylogenetic tree object into a MATLAB figure as a
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% phylogram. The significant distances between branches and nodes are in
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% horizontal direction, vertical coordinates are accommodated only for
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% display purposes. Handles to graph elements are stored in the
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% 'UserData' figure field, such that graphic properties can be easily
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% modified.
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%
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% PLOT(TREE,ACTIVEBRANCHES) hides the non'active branches and all their
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% descendants. ACTIVEBRANCHES is a logical array of size
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% [numBranches x 1] indicating the active branches.
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%
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% PLOT(...,'TYPE',type) selects the method to render the phylogenetic
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% tree. Options are: 'square' (default), 'angular', and 'radial'.
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%
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% PLOT(...,'ORIENTATION',orient) will orient the phylogenetic tree within
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% the figure window. Options are: 'top', 'bottom', 'left' (default), and,
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% 'right'. Orientation parameter is valid only for phylograms or
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% cladograms.
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%
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% PLOT(...,'BRANCHLABELS',value) hides/unhides branch labels. Options are
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% true or false. Branch labels are placed next to the branch node.
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% Defaults to false (true) when TYPE is (is not) 'radial'.
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%
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% PLOT(...,'LEAFLABELS',value) hides/unhides leaf labels. Options are
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% true or false. Leaf labels are placed next to the leaf nodes. Defaults
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% to false (true) when TYPE is (is not) 'radial'.
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%
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% PLOT(...,'TERMINALLABELS',value) hides/unhides terminal labels. Options
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% are true (default) or false. Terminal labels are placed over the axis
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% tick labels, ignored when 'radial' type is used.
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%
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% H = PLOT(...) returns a structure with handles to the graph elements.
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%
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% Example:
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%
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% tr = phytreeread('pf00002.tree')
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% plot(tr,'type','radial')
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%
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% % Graph element properties can be modified as follows:
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%
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% h=get(gcf,'UserData')
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% set(h.branchNodeLabels,'FontSize',6,'Color',[.5 .5 .5])
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%
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% See also PHYTREE, PHYTREE/VIEW, PHYTREEREAD, PHYTREETOOL, SEQLINKAGE.
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% Copyright 2003-2006 The MathWorks, Inc.
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% $Revision: 1.1.6.10 $ $Author: batserve $ $Date: 2006/06/16 20:06:45 $
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if numel(tr)~=1
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error('Bioinfo:phytree:plot:NoMultielementArrays',...
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'Phylogenetic tree must be an 1-by-1 object.');
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end
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% set defaults
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dispBranchLabels = NaN;
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dispLeafLabels = NaN;
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dispTerminalLabels = true;
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renderType = 'square';
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orientation = 'left';
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rotation = 0;
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tr = struct(tr);
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tr.numBranches = size(tr.tree,1);
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if nargin>1 && islogical(varargin{1})
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activeBranches = varargin{1};
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argStart = 2;
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else
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activeBranches = true(tr.numBranches,1);
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argStart = 1;
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end
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if nargin - argStart > 0
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if rem(nargin - argStart,2) == 1
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error('Bioinfo:phytree:plot:IncorrectNumberOfArguments',...
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'Incorrect number of arguments to %s.',mfilename);
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end
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okargs = {'type','orientation','rotation',...
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'branchlabels','leaflabels','terminallabels'};
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for j = argStart:2:nargin-argStart
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pname = varargin{j};
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pval = varargin{j+1};
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k = find(strncmpi(pname,okargs,numel(pname)));
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if isempty(k)
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error('Bioinfo:phytree:plot: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:plot: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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case 1 % type
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oktypes={'square','angular','radial'};
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l = strmatch(lower(pval),oktypes); %#ok
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if isempty(l)
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error('Bioinfo:phytree:plot:UnknownTypeName',...
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'Unknown option for %s.',upper(okargs{k}));
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else
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if l==4
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l=1;
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end
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renderType = oktypes{l};
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end
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case 2 % orientation
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oktypes={'left','right','top','bottom'};
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l = strmatch(lower(pval),oktypes); %#ok
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if isempty(l)
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error('Bioinfo:phytree:plot:UnknownOrientation',...
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'Unknown option for %s.',upper(okargs{k}));
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else
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orientation = oktypes{l};
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end
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case 3 % rotation
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if isreal(pval(1))
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rotation = double(pval(1));
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else
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error('Bioinfo:phytree:plot:NotValidType',...
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'ROTATION must be numeric and real');
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end
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case 4 % branch labels
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dispBranchLabels = opttf(pval);
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case 5 % leaf labels
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dispLeafLabels = opttf(pval);
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case 6 % terminal labels
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dispTerminalLabels = opttf(pval);
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end
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end
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end
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end
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% set dependent defaults
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if isnan(dispBranchLabels)
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if isequal(renderType,'radial')
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dispBranchLabels = true;
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else
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dispBranchLabels = false;
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end
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end
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if isnan(dispLeafLabels)
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if isequal(renderType,'radial')
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dispLeafLabels = true;
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else
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dispLeafLabels = false;
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end
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end
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tr = doBasicCalculations(tr,activeBranches,renderType);
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nodeIndex = 1:tr.numLabels;
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leafIndex = 1:tr.numLeaves;
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branchIndex = tr.numLeaves+1:tr.numLabels;
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% check empty names
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for ind = nodeIndex
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if isempty(tr.names{ind})
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if ind > tr.numLeaves
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tr.names{ind} = ['Branch ' num2str(ind-tr.numLeaves)];
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else
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tr.names{ind} = ['Leaf ' num2str(ind)];
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end
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end
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end
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% rendering graphic objects
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fig = gcf;
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% fig = figure('Renderer','ZBuffer');
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h.fig = fig;
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h.axes = axes; hold on;
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sepUnit = max(tr.x)*[-1/20 21/20];
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% setting the axes
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switch renderType
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case {'square','angular'}
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switch orientation
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case 'left'
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set(h.axes,'YTick',1:numel(tr.terminalNodes),'Ydir','reverse',...
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'YtickLabel','','YAxisLocation','Right')
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if dispTerminalLabels
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set(h.axes,'Position',[.05 .10 .7 .85])
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else
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set(h.axes,'Position',[.05 .10 .9 .85])
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end
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xlim(sepUnit);
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ylim([0 numel(tr.terminalNodes)+1]);
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case 'right'
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set(h.axes,'YTick',1:numel(tr.terminalNodes),'Xdir','reverse','Ydir','reverse',...
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'YtickLabel','','YAxisLocation','Left')
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if dispTerminalLabels
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set(h.axes,'Position',[.25 .10 .7 .85])
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else
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set(h.axes,'Position',[.05 .10 .9 .85])
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end
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xlim(sepUnit);
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ylim([0 numel(tr.terminalNodes)+1]);
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case 'top'
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set(h.axes,'XTick',1:numel(tr.terminalNodes),...
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'XtickLabel','','XAxisLocation','Top')
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if dispTerminalLabels
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set(h.axes,'Position',[.10 .05 .85 .7])
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else
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set(h.axes,'Position',[.10 .05 .85 .9])
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end
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ylim(sepUnit);
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xlim([0 numel(tr.terminalNodes)+1]);
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case 'bottom'
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set(h.axes,'XTick',1:numel(tr.terminalNodes),'Ydir','reverse',...
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'XtickLabel','','XAxisLocation','Bottom')
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if dispTerminalLabels
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set(h.axes,'Position',[.10 .25 .85 .7])
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else
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set(h.axes,'Position',[.10 .05 .85 .9])
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end
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ylim(sepUnit);
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xlim([0 numel(tr.terminalNodes)+1]);
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end
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case 'radial'
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set(h.axes,'XTick',[],'YTick',[])
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set(h.axes,'Position',[.05 .05 .9 .9])
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dispTerminalLabels = false;
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axis equal
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end
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% drawing lines
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switch renderType
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case 'square'
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X = tr.x([nodeIndex;repmat([tr.par(1:tr.numLabels-1) tr.numLabels],2,1)]);
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Y = tr.y([repmat(nodeIndex,2,1);[tr.par(1:tr.numLabels-1) tr.numLabels]]);
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switch orientation
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case {'left','right'}
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h.BranchLines = plot(X,Y,'-k');
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delete(h.BranchLines(~tr.activeNodes))
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h.BranchLines = h.BranchLines(tr.activeNodes);
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case {'top','bottom'}
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h.BranchLines = plot(Y,X,'-k');
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delete(h.BranchLines(~tr.activeNodes))
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h.BranchLines = h.BranchLines(tr.activeNodes);
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end
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case 'angular'
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X = tr.x([nodeIndex;[tr.par(1:tr.numLabels-1) tr.numLabels]]);
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Y = tr.y([nodeIndex;[tr.par(1:tr.numLabels-1) tr.numLabels]]);
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switch orientation
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case {'left','right'}
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h.BranchLines = plot(X,Y,'-k');
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delete(h.BranchLines(~tr.activeNodes))
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h.BranchLines = h.BranchLines(tr.activeNodes);
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case {'top','bottom'}
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h.BranchLines = plot(Y,X,'-k');
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delete(h.BranchLines(~tr.activeNodes))
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h.BranchLines = h.BranchLines(tr.activeNodes);
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end
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case 'radial'
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R = tr.x;
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A = tr.y / numel(tr.terminalNodes)*2*pi+rotation*pi/180;
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tr.x = R .* sin(A);
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tr.y = R .* cos(A);
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X = tr.x([nodeIndex;[tr.par(1:tr.numLabels-1) tr.numLabels]]);
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Y = tr.y([nodeIndex;[tr.par(1:tr.numLabels-1) tr.numLabels]]);
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h.BranchLines = plot(X,Y,'-k');
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delete(h.BranchLines(~tr.activeNodes))
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h.BranchLines = h.BranchLines(tr.activeNodes);
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end
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% drawing nodes
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switch renderType
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case {'square','angular'}
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switch orientation
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case {'left','right'}
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h.BranchDots = plot(tr.x(branchIndex(tr.activeNodes(branchIndex))),...
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tr.y(branchIndex(tr.activeNodes(branchIndex))),'o',...
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'MarkerSize',5,'MarkerEdgeColor','k',...
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'MarkerFaceColor','b');
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h.LeafDots = plot(tr.x(leafIndex(tr.activeNodes(leafIndex))),...
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tr.y(leafIndex(tr.activeNodes(leafIndex))),'square',...
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'MarkerSize',4,'MarkerEdgeColor','k',...
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'MarkerFaceColor','w');
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case {'top','bottom'}
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h.BranchDots = plot(tr.y(branchIndex(tr.activeNodes(branchIndex))),...
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tr.x(branchIndex(tr.activeNodes(branchIndex))),'o',...
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'MarkerSize',5,'MarkerEdgeColor','k',...
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'MarkerFaceColor','b');
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h.LeafDots = plot(tr.y(leafIndex(tr.activeNodes(leafIndex))),...
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tr.x(leafIndex(tr.activeNodes(leafIndex))),'square',...
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'MarkerSize',4,'MarkerEdgeColor','k',...
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'MarkerFaceColor','w');
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end
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case 'radial'
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h.BranchDots = plot(tr.x(branchIndex(tr.activeNodes(branchIndex))),...
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tr.y(branchIndex(tr.activeNodes(branchIndex))),'o',...
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'MarkerSize',5,'MarkerEdgeColor','k',...
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'MarkerFaceColor','b');
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h.LeafDots = plot(tr.x(leafIndex(tr.activeNodes(leafIndex))),...
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tr.y(leafIndex(tr.activeNodes(leafIndex))),'square',...
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'MarkerSize',4,'MarkerEdgeColor','k',...
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'MarkerFaceColor','w');
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end
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% resize figure if needed
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switch renderType
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case {'square','angular'}
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switch orientation
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case {'left','right'}
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correctFigureSize(fig, 15 * numel(tr.terminalNodes),0);
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fontRatio = max(get(fig,'Position').*[0 0 0 1])/numel(tr.terminalNodes);
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case {'top','bottom'}
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correctFigureSize(fig, 0, 15 * numel(tr.terminalNodes));
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fontRatio = max(get(fig,'Position').*[0 0 1 0])/numel(tr.terminalNodes);
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end
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case 'radial'
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temp = 10/pi*numel(tr.terminalNodes);
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correctFigureSize(fig,temp,temp);
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fontRatio = max(get(fig,'Position').*[0 0 1 0])/numel(tr.terminalNodes);
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end
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set(h.axes,'Fontsize',min(9,ceil(fontRatio/1.5)));
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% set branch node labels
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X = tr.x(branchIndex(tr.activeNodes(tr.numLeaves+1:tr.numLabels)));
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Y = tr.y(branchIndex(tr.activeNodes(tr.numLeaves+1:tr.numLabels)));
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switch renderType
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case {'square','angular'}
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switch orientation
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case {'left'}
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h.branchNodeLabels = text(X+sepUnit(1)/2,Y,tr.names(branchIndex(tr.activeNodes(tr.numLeaves+1:tr.numLabels))));
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set(h.branchNodeLabels,'color',[0 0 .8],'clipping','on')
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set(h.branchNodeLabels,'vertical','bottom')
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set(h.branchNodeLabels,'horizontal','right')
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set(h.branchNodeLabels,'Fontsize',min(8,ceil(fontRatio/2)));
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case {'right'}
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h.branchNodeLabels = text(X+sepUnit(1)/2,Y,tr.names(branchIndex(tr.activeNodes(tr.numLeaves+1:tr.numLabels))));
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set(h.branchNodeLabels,'color',[0 0 .8],'clipping','on')
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set(h.branchNodeLabels,'vertical','bottom')
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set(h.branchNodeLabels,'Fontsize',min(8,ceil(fontRatio/2)));
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case {'top'}
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h.branchNodeLabels = text(Y,X-sepUnit(1)/2,tr.names(branchIndex(tr.activeNodes(tr.numLeaves+1:tr.numLabels))));
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set(h.branchNodeLabels,'color',[0 0 .8],'clipping','on')
|
||
|
|
set(h.branchNodeLabels,'vertical','bottom','Rotation',30)
|
||
|
|
set(h.branchNodeLabels,'Fontsize',min(8,ceil(fontRatio/2)));
|
||
|
|
case {'bottom'}
|
||
|
|
h.branchNodeLabels = text(Y,X+sepUnit(1)/2,tr.names(branchIndex(tr.activeNodes(tr.numLeaves+1:tr.numLabels))));
|
||
|
|
set(h.branchNodeLabels,'color',[0 0 .8],'clipping','on')
|
||
|
|
set(h.branchNodeLabels,'vertical','bottom','Rotation',30)
|
||
|
|
set(h.branchNodeLabels,'Fontsize',min(8,ceil(fontRatio/2)));
|
||
|
|
end
|
||
|
|
case 'radial'
|
||
|
|
h.branchNodeLabels = text(X,Y,tr.names(branchIndex(tr.activeNodes(tr.numLeaves+1:tr.numLabels))));
|
||
|
|
set(h.branchNodeLabels,'color',[0 0 .8],'clipping','on')
|
||
|
|
set(h.branchNodeLabels,'vertical','bottom')
|
||
|
|
set(h.branchNodeLabels,'Fontsize',min(8,ceil(fontRatio*1.2)));
|
||
|
|
for ind = 1:numel(h.branchNodeLabels)
|
||
|
|
if X(ind)<0
|
||
|
|
set(h.branchNodeLabels(ind),'horizontal','right')
|
||
|
|
set(h.branchNodeLabels(ind),'Position',get(h.branchNodeLabels(ind),'Position')+[sepUnit(1)/2 0 0])
|
||
|
|
else
|
||
|
|
set(h.branchNodeLabels(ind),'horizontal','left')
|
||
|
|
set(h.branchNodeLabels(ind),'Position',get(h.branchNodeLabels(ind),'Position')-[sepUnit(1)/2 0 0])
|
||
|
|
end
|
||
|
|
end
|
||
|
|
end
|
||
|
|
|
||
|
|
% set leaf nodes labels
|
||
|
|
X = tr.x(leafIndex(tr.activeNodes(1:tr.numLeaves)));
|
||
|
|
Y = tr.y(leafIndex(tr.activeNodes(1:tr.numLeaves)));
|
||
|
|
switch renderType
|
||
|
|
case {'square','angular'}
|
||
|
|
switch orientation
|
||
|
|
case {'left'}
|
||
|
|
h.leafNodeLabels = text(X-sepUnit(1)/2,Y,tr.names(leafIndex(tr.activeNodes(1:tr.numLeaves))));
|
||
|
|
set(h.leafNodeLabels,'color',[.5 .5 .5],'clipping','on')
|
||
|
|
set(h.leafNodeLabels,'horizontal','left')
|
||
|
|
set(h.leafNodeLabels,'Fontsize',min(8,ceil(fontRatio/2)));
|
||
|
|
case {'right'}
|
||
|
|
h.leafNodeLabels = text(X-sepUnit(1)/2,Y,tr.names(leafIndex(tr.activeNodes(1:tr.numLeaves))));
|
||
|
|
set(h.leafNodeLabels,'color',[.5 .5 .5],'clipping','on')
|
||
|
|
set(h.leafNodeLabels,'horizontal','right')
|
||
|
|
set(h.leafNodeLabels,'Fontsize',min(8,ceil(fontRatio/2)));
|
||
|
|
case {'top'}
|
||
|
|
h.leafNodeLabels = text(Y,X-sepUnit(1)/2,tr.names(leafIndex(tr.activeNodes(1:tr.numLeaves))));
|
||
|
|
set(h.leafNodeLabels,'color',[.5 .5 .5],'clipping','on')
|
||
|
|
set(h.leafNodeLabels,'horizontal','left','Rotation',60)
|
||
|
|
set(h.leafNodeLabels,'Fontsize',min(8,ceil(fontRatio/2)));
|
||
|
|
case {'bottom'}
|
||
|
|
h.leafNodeLabels = text(Y,X-sepUnit(1),tr.names(leafIndex(tr.activeNodes(1:tr.numLeaves))));
|
||
|
|
set(h.leafNodeLabels,'color',[.5 .5 .5],'clipping','on')
|
||
|
|
set(h.leafNodeLabels,'horizontal','right','Rotation',60)
|
||
|
|
set(h.leafNodeLabels,'Fontsize',min(8,ceil(fontRatio/2)));
|
||
|
|
end
|
||
|
|
case 'radial'
|
||
|
|
h.leafNodeLabels = text(X,Y,tr.names(leafIndex(tr.activeNodes(1:tr.numLeaves))));
|
||
|
|
set(h.leafNodeLabels,'color',[.5 .5 .5],'clipping','on')
|
||
|
|
set(h.leafNodeLabels,'Fontsize',min(8,ceil(fontRatio*1.2)));
|
||
|
|
% textHeight = mean(cell2mat(get(h.leafNodeLabels,'Extent')))*[0 0 0 1]';
|
||
|
|
for ind = 1:numel(h.leafNodeLabels)
|
||
|
|
if X(ind)<0
|
||
|
|
set(h.leafNodeLabels(ind),'horizontal','right')
|
||
|
|
set(h.leafNodeLabels(ind),'Position',get(h.leafNodeLabels(ind),'Position')+[sepUnit(1) 0 0])
|
||
|
|
else
|
||
|
|
set(h.leafNodeLabels(ind),'horizontal','left')
|
||
|
|
set(h.leafNodeLabels(ind),'Position',get(h.leafNodeLabels(ind),'Position')-[sepUnit(1) 0 0])
|
||
|
|
end
|
||
|
|
% a=atan(Y(ind)/X(ind))*180/pi;
|
||
|
|
% if a > 0 a = max(0,a-60)/2; else
|
||
|
|
% a = min(0,a+60)/2; end
|
||
|
|
% set(h.leafNodeLabels(ind),'Rotation',a)
|
||
|
|
end
|
||
|
|
[sortedY,hsY]=sort(Y);
|
||
|
|
idx=hsY(X(hsY)>0 & sortedY>0);
|
||
|
|
if numel(idx)
|
||
|
|
extentY = get(h.leafNodeLabels(idx(1)),'Extent')*[0;0;0;1];
|
||
|
|
positionY = get(h.leafNodeLabels(idx(1)),'Position')*[0;1;0];
|
||
|
|
for i = 2:numel(idx)
|
||
|
|
position = get(h.leafNodeLabels(idx(i)),'Position');
|
||
|
|
positionY = max(positionY+extentY,position(2));
|
||
|
|
position(2) = positionY;
|
||
|
|
set(h.leafNodeLabels(idx(i)),'Position',position)
|
||
|
|
end
|
||
|
|
end
|
||
|
|
idx=hsY(X(hsY)<0 & sortedY>0);
|
||
|
|
if numel(idx)
|
||
|
|
extentY = get(h.leafNodeLabels(idx(1)),'Extent')*[0;0;0;1];
|
||
|
|
positionY = get(h.leafNodeLabels(idx(1)),'Position')*[0;1;0];
|
||
|
|
for i = 2:numel(idx)
|
||
|
|
position = get(h.leafNodeLabels(idx(i)),'Position');
|
||
|
|
positionY = max(positionY+extentY,position(2));
|
||
|
|
position(2) = positionY;
|
||
|
|
set(h.leafNodeLabels(idx(i)),'Position',position)
|
||
|
|
end
|
||
|
|
end
|
||
|
|
idx=flipud(hsY(X(hsY)>0 & sortedY<0));
|
||
|
|
if numel(idx)
|
||
|
|
extentY = get(h.leafNodeLabels(idx(1)),'Extent')*[0;0;0;1];
|
||
|
|
positionY = get(h.leafNodeLabels(idx(1)),'Position')*[0;1;0];
|
||
|
|
for i = 2:numel(idx)
|
||
|
|
position = get(h.leafNodeLabels(idx(i)),'Position');
|
||
|
|
positionY = min(positionY-extentY,position(2));
|
||
|
|
position(2) = positionY;
|
||
|
|
set(h.leafNodeLabels(idx(i)),'Position',position)
|
||
|
|
end
|
||
|
|
end
|
||
|
|
idx=flipud(hsY(X(hsY)<0 & sortedY<0));
|
||
|
|
if numel(idx)
|
||
|
|
extentY = get(h.leafNodeLabels(idx(1)),'Extent')*[0;0;0;1];
|
||
|
|
positionY = get(h.leafNodeLabels(idx(1)),'Position')*[0;1;0];
|
||
|
|
for i = 2:numel(idx)
|
||
|
|
position = get(h.leafNodeLabels(idx(i)),'Position');
|
||
|
|
positionY = min(positionY-extentY,position(2));
|
||
|
|
position(2) = positionY;
|
||
|
|
set(h.leafNodeLabels(idx(i)),'Position',position)
|
||
|
|
end
|
||
|
|
end
|
||
|
|
|
||
|
|
end
|
||
|
|
|
||
|
|
% correct axis limits given the extent of labels
|
||
|
|
if dispBranchLabels
|
||
|
|
E = cell2mat(get(h.branchNodeLabels,'Extent'));
|
||
|
|
if strcmp(get(gca,'XDir'),'reverse')
|
||
|
|
E(:,1) = E(:,1) - E(:,3);
|
||
|
|
end
|
||
|
|
if strcmp(get(gca,'YDir'),'reverse')
|
||
|
|
E(:,2) = E(:,2) - E(:,4);
|
||
|
|
end
|
||
|
|
E=[E;[xlim*[1;0] ylim*[1;0] diff(xlim) diff(ylim)]];
|
||
|
|
mins = min(E(:,[1 2]));
|
||
|
|
maxs = max([sum(E(:,[1 3]),2) sum(E(:,[2 4]),2)]);
|
||
|
|
axis([mins(1) maxs(1) mins(2) maxs(2)])
|
||
|
|
end
|
||
|
|
|
||
|
|
if dispLeafLabels
|
||
|
|
E = cell2mat(get(h.leafNodeLabels,'Extent'));
|
||
|
|
if strcmp(get(gca,'XDir'),'reverse')
|
||
|
|
E(:,1) = E(:,1) - E(:,3);
|
||
|
|
end
|
||
|
|
if strcmp(get(gca,'YDir'),'reverse')
|
||
|
|
E(:,2) = E(:,2) - E(:,4);
|
||
|
|
end
|
||
|
|
E=[E;[xlim*[1;0] ylim*[1;0] diff(xlim) diff(ylim)]];
|
||
|
|
mins = min(E(:,[1 2]));
|
||
|
|
maxs = max([sum(E(:,[1 3]),2) sum(E(:,[2 4]),2)]);
|
||
|
|
axis([mins(1) maxs(1) mins(2) maxs(2)])
|
||
|
|
end
|
||
|
|
|
||
|
|
% set terminal nodes labels
|
||
|
|
switch renderType
|
||
|
|
case {'square','angular'}
|
||
|
|
X = tr.x(tr.terminalNodes) * 0;
|
||
|
|
Y = tr.y(tr.terminalNodes);
|
||
|
|
switch orientation
|
||
|
|
case {'left'}
|
||
|
|
X = X + max(xlim) - sepUnit(1)/2;
|
||
|
|
h.terminalNodeLabels = text(X,Y,tr.names(tr.terminalNodes));
|
||
|
|
case {'right'}
|
||
|
|
X = X + max(xlim) - sepUnit(1)/2;
|
||
|
|
h.terminalNodeLabels = text(X,Y,tr.names(tr.terminalNodes));
|
||
|
|
set(h.terminalNodeLabels,'Horizontal','right')
|
||
|
|
case {'top'}
|
||
|
|
X = X + max(ylim) - sepUnit(1)/2;
|
||
|
|
h.terminalNodeLabels = text(Y,X,tr.names(tr.terminalNodes));
|
||
|
|
set(h.terminalNodeLabels,'Rotation',90)
|
||
|
|
case {'bottom'}
|
||
|
|
X = X + max(ylim) - sepUnit(1)/2;
|
||
|
|
h.terminalNodeLabels = text(Y,X,tr.names(tr.terminalNodes));
|
||
|
|
set(h.terminalNodeLabels,'Rotation',270)
|
||
|
|
end
|
||
|
|
case 'radial'
|
||
|
|
h.terminalNodeLabels = text(0,0,' ');
|
||
|
|
end
|
||
|
|
|
||
|
|
if dispTerminalLabels
|
||
|
|
set(h.terminalNodeLabels,'Fontsize',min(9,ceil(fontRatio/1.5)));
|
||
|
|
end
|
||
|
|
|
||
|
|
if ~dispBranchLabels
|
||
|
|
set(h.branchNodeLabels,'visible','off');
|
||
|
|
end
|
||
|
|
if ~dispLeafLabels
|
||
|
|
set(h.leafNodeLabels,'visible','off');
|
||
|
|
end
|
||
|
|
if ~dispTerminalLabels
|
||
|
|
set(h.terminalNodeLabels,'visible','off');
|
||
|
|
end
|
||
|
|
|
||
|
|
box on
|
||
|
|
hold off
|
||
|
|
|
||
|
|
% store handles
|
||
|
|
set(fig,'UserData',h)
|
||
|
|
if nargout
|
||
|
|
handles = h;
|
||
|
|
end
|
||
|
|
|
||
|
|
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||
|
|
function tr = doBasicCalculations(tr,activeBranches,renderType)
|
||
|
|
|
||
|
|
% helper function to compute and find some features of the tree
|
||
|
|
tr.numLeaves = tr.numBranches + 1;
|
||
|
|
tr.numLabels = tr.numBranches + tr.numLeaves;
|
||
|
|
|
||
|
|
% remove uderscores from names
|
||
|
|
for ind = 1:tr.numLabels
|
||
|
|
tr.names{ind}(tr.names{ind}=='_')=' ';
|
||
|
|
end
|
||
|
|
|
||
|
|
% obtain parents for every node
|
||
|
|
tr.par(tr.tree(:)) = tr.numLeaves + [1:tr.numBranches 1:tr.numBranches];
|
||
|
|
|
||
|
|
% find active nodes
|
||
|
|
tr.activeNodes = true(tr.numLabels,1);
|
||
|
|
for ind =tr.numBranches:-1:1
|
||
|
|
tr.activeNodes(tr.tree(ind,:)) = tr.activeNodes(tr.numLeaves+ind) & activeBranches(ind);
|
||
|
|
end
|
||
|
|
|
||
|
|
% propagate last leaf
|
||
|
|
tr.lastleaf = 1:tr.numLabels;
|
||
|
|
for ind = tr.numBranches:-1:1
|
||
|
|
if ~tr.activeNodes(tr.tree(ind,1))
|
||
|
|
tr.lastleaf(tr.tree(ind,:))=tr.lastleaf(ind+tr.numLeaves);
|
||
|
|
end
|
||
|
|
end
|
||
|
|
|
||
|
|
tr.activeBranches = tr.activeNodes(tr.numLeaves+1:tr.numLabels)&activeBranches;
|
||
|
|
tr.activeLeaves = tr.activeNodes(1:tr.numLeaves);
|
||
|
|
|
||
|
|
% find x coordinates of branches
|
||
|
|
tr.x = tr.dist;
|
||
|
|
for ind = tr.numBranches:-1:1
|
||
|
|
tr.x(tr.tree(ind,:)) = tr.x(tr.tree(ind,:)) + tr.x(ind+tr.numLeaves);
|
||
|
|
end
|
||
|
|
|
||
|
|
% find y coordinates of branches
|
||
|
|
tr.terminalNodes = tr.lastleaf([true,diff(tr.lastleaf(1:tr.numLeaves))~=0]);
|
||
|
|
tr.y=zeros(tr.numLabels,1);
|
||
|
|
tr.y(tr.terminalNodes)=1:length(tr.terminalNodes);
|
||
|
|
switch renderType
|
||
|
|
case 'square'
|
||
|
|
for ind = 1:tr.numBranches
|
||
|
|
if tr.activeBranches(ind)
|
||
|
|
tr.y(ind+tr.numLeaves) = mean(tr.y(tr.tree(ind,:)));
|
||
|
|
end
|
||
|
|
end
|
||
|
|
case {'angular','radial'}
|
||
|
|
for ind = 1:tr.numBranches
|
||
|
|
if tr.activeBranches(ind)
|
||
|
|
if tr.x(tr.tree(ind,1))/tr.x(tr.tree(ind,2))>3
|
||
|
|
tr.y(ind+tr.numLeaves) = tr.y(tr.tree(ind,1));
|
||
|
|
elseif tr.x(tr.tree(ind,2))/tr.x(tr.tree(ind,1))>3
|
||
|
|
tr.y(ind+tr.numLeaves) = tr.y(tr.tree(ind,2));
|
||
|
|
else
|
||
|
|
tr.y(ind+tr.numLeaves) = mean(tr.y(tr.tree(ind,:)));
|
||
|
|
end
|
||
|
|
end
|
||
|
|
end
|
||
|
|
end
|
||
|
|
|
||
|
|
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||
|
|
function correctFigureSize(fig,recommendedHeight,recommendedWidth)
|
||
|
|
% helper function to increase initial figure size depending on the screen &
|
||
|
|
% tree sizes
|
||
|
|
screenSize = diff(reshape(get(0,'ScreenSize'),2,2),[],2)-[0;100];
|
||
|
|
% 100 gives extra space for the figure header and win toolbar
|
||
|
|
position = get(fig,'Position');
|
||
|
|
if recommendedHeight > position(4)
|
||
|
|
if recommendedHeight < sum(position([2 4]))
|
||
|
|
position(2) = sum(position([2 4])) - recommendedHeight;
|
||
|
|
position(4) = recommendedHeight;
|
||
|
|
elseif recommendedHeight < screenSize(2)
|
||
|
|
position(2) = 30;
|
||
|
|
position(4) = recommendedHeight;
|
||
|
|
else
|
||
|
|
position(2) = 30;
|
||
|
|
position(4) = screenSize(2);
|
||
|
|
end
|
||
|
|
end
|
||
|
|
if recommendedWidth > position(3)
|
||
|
|
if recommendedWidth < sum(position([1 3]))
|
||
|
|
position(1) = sum(position([1 3])) - recommendedWidth;
|
||
|
|
position(3) = recommendedWidth;
|
||
|
|
elseif recommendedWidth < screenSize(1)
|
||
|
|
position(1) = 0;
|
||
|
|
position(3) = recommendedHeight;
|
||
|
|
else
|
||
|
|
position(1) = 0;
|
||
|
|
position(3) = screenSize(1);
|
||
|
|
end
|
||
|
|
end
|
||
|
|
set(fig,'Position',position)
|