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Added source Matlab code for reference

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Waldir Leoncio 2019-12-16 16:47:21 +01:00
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commit b5d99903d2
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function handles = Plot(tr,varargin)
%PLOT renders a phylogenetic tree.
%
% PLOT(TREE) renders a phylogenetic tree object into a MATLAB figure as a
% phylogram. The significant distances between branches and nodes are in
% horizontal direction, vertical coordinates are accommodated only for
% display purposes. Handles to graph elements are stored in the
% 'UserData' figure field, such that graphic properties can be easily
% modified.
%
% PLOT(TREE,ACTIVEBRANCHES) hides the non'active branches and all their
% descendants. ACTIVEBRANCHES is a logical array of size
% [numBranches x 1] indicating the active branches.
%
% PLOT(...,'TYPE',type) selects the method to render the phylogenetic
% tree. Options are: 'square' (default), 'angular', and 'radial'.
%
% PLOT(...,'ORIENTATION',orient) will orient the phylogenetic tree within
% the figure window. Options are: 'top', 'bottom', 'left' (default), and,
% 'right'. Orientation parameter is valid only for phylograms or
% cladograms.
%
% PLOT(...,'BRANCHLABELS',value) hides/unhides branch labels. Options are
% true or false. Branch labels are placed next to the branch node.
% Defaults to false (true) when TYPE is (is not) 'radial'.
%
% PLOT(...,'LEAFLABELS',value) hides/unhides leaf labels. Options are
% true or false. Leaf labels are placed next to the leaf nodes. Defaults
% to false (true) when TYPE is (is not) 'radial'.
%
% PLOT(...,'TERMINALLABELS',value) hides/unhides terminal labels. Options
% are true (default) or false. Terminal labels are placed over the axis
% tick labels, ignored when 'radial' type is used.
%
% H = PLOT(...) returns a structure with handles to the graph elements.
%
% Example:
%
% tr = phytreeread('pf00002.tree')
% plot(tr,'type','radial')
%
% % Graph element properties can be modified as follows:
%
% h=get(gcf,'UserData')
% set(h.branchNodeLabels,'FontSize',6,'Color',[.5 .5 .5])
%
% See also PHYTREE, PHYTREE/VIEW, PHYTREEREAD, PHYTREETOOL, SEQLINKAGE.
% Copyright 2003-2006 The MathWorks, Inc.
% $Revision: 1.1.6.10 $ $Author: batserve $ $Date: 2006/06/16 20:06:45 $
if numel(tr)~=1
error('Bioinfo:phytree:plot:NoMultielementArrays',...
'Phylogenetic tree must be an 1-by-1 object.');
end
% set defaults
dispBranchLabels = NaN;
dispLeafLabels = NaN;
dispTerminalLabels = true;
renderType = 'square';
orientation = 'left';
rotation = 0;
tr = struct(tr);
tr.numBranches = size(tr.tree,1);
if nargin>1 && islogical(varargin{1})
activeBranches = varargin{1};
argStart = 2;
else
activeBranches = true(tr.numBranches,1);
argStart = 1;
end
if nargin - argStart > 0
if rem(nargin - argStart,2) == 1
error('Bioinfo:phytree:plot:IncorrectNumberOfArguments',...
'Incorrect number of arguments to %s.',mfilename);
end
okargs = {'type','orientation','rotation',...
'branchlabels','leaflabels','terminallabels'};
for j = argStart:2:nargin-argStart
pname = varargin{j};
pval = varargin{j+1};
k = find(strncmpi(pname,okargs,numel(pname)));
if isempty(k)
error('Bioinfo:phytree:plot:UnknownParameterName',...
'Unknown parameter name: %s.',pname);
elseif length(k)>1
error('Bioinfo:phytree:plot:AmbiguousParameterName',...
'Ambiguous parameter name: %s.',pname);
else
switch(k)
case 1 % type
oktypes={'square','angular','radial'};
l = strmatch(lower(pval),oktypes); %#ok
if isempty(l)
error('Bioinfo:phytree:plot:UnknownTypeName',...
'Unknown option for %s.',upper(okargs{k}));
else
if l==4
l=1;
end
renderType = oktypes{l};
end
case 2 % orientation
oktypes={'left','right','top','bottom'};
l = strmatch(lower(pval),oktypes); %#ok
if isempty(l)
error('Bioinfo:phytree:plot:UnknownOrientation',...
'Unknown option for %s.',upper(okargs{k}));
else
orientation = oktypes{l};
end
case 3 % rotation
if isreal(pval(1))
rotation = double(pval(1));
else
error('Bioinfo:phytree:plot:NotValidType',...
'ROTATION must be numeric and real');
end
case 4 % branch labels
dispBranchLabels = opttf(pval);
case 5 % leaf labels
dispLeafLabels = opttf(pval);
case 6 % terminal labels
dispTerminalLabels = opttf(pval);
end
end
end
end
% set dependent defaults
if isnan(dispBranchLabels)
if isequal(renderType,'radial')
dispBranchLabels = true;
else
dispBranchLabels = false;
end
end
if isnan(dispLeafLabels)
if isequal(renderType,'radial')
dispLeafLabels = true;
else
dispLeafLabels = false;
end
end
tr = doBasicCalculations(tr,activeBranches,renderType);
nodeIndex = 1:tr.numLabels;
leafIndex = 1:tr.numLeaves;
branchIndex = tr.numLeaves+1:tr.numLabels;
% check empty names
for ind = nodeIndex
if isempty(tr.names{ind})
if ind > tr.numLeaves
tr.names{ind} = ['Branch ' num2str(ind-tr.numLeaves)];
else
tr.names{ind} = ['Leaf ' num2str(ind)];
end
end
end
% rendering graphic objects
fig = gcf;
% fig = figure('Renderer','ZBuffer');
h.fig = fig;
h.axes = axes; hold on;
sepUnit = max(tr.x)*[-1/20 21/20];
% setting the axes
switch renderType
case {'square','angular'}
switch orientation
case 'left'
set(h.axes,'YTick',1:numel(tr.terminalNodes),'Ydir','reverse',...
'YtickLabel','','YAxisLocation','Right')
if dispTerminalLabels
set(h.axes,'Position',[.05 .10 .7 .85])
else
set(h.axes,'Position',[.05 .10 .9 .85])
end
xlim(sepUnit);
ylim([0 numel(tr.terminalNodes)+1]);
case 'right'
set(h.axes,'YTick',1:numel(tr.terminalNodes),'Xdir','reverse','Ydir','reverse',...
'YtickLabel','','YAxisLocation','Left')
if dispTerminalLabels
set(h.axes,'Position',[.25 .10 .7 .85])
else
set(h.axes,'Position',[.05 .10 .9 .85])
end
xlim(sepUnit);
ylim([0 numel(tr.terminalNodes)+1]);
case 'top'
set(h.axes,'XTick',1:numel(tr.terminalNodes),...
'XtickLabel','','XAxisLocation','Top')
if dispTerminalLabels
set(h.axes,'Position',[.10 .05 .85 .7])
else
set(h.axes,'Position',[.10 .05 .85 .9])
end
ylim(sepUnit);
xlim([0 numel(tr.terminalNodes)+1]);
case 'bottom'
set(h.axes,'XTick',1:numel(tr.terminalNodes),'Ydir','reverse',...
'XtickLabel','','XAxisLocation','Bottom')
if dispTerminalLabels
set(h.axes,'Position',[.10 .25 .85 .7])
else
set(h.axes,'Position',[.10 .05 .85 .9])
end
ylim(sepUnit);
xlim([0 numel(tr.terminalNodes)+1]);
end
case 'radial'
set(h.axes,'XTick',[],'YTick',[])
set(h.axes,'Position',[.05 .05 .9 .9])
dispTerminalLabels = false;
axis equal
end
% drawing lines
switch renderType
case 'square'
X = tr.x([nodeIndex;repmat([tr.par(1:tr.numLabels-1) tr.numLabels],2,1)]);
Y = tr.y([repmat(nodeIndex,2,1);[tr.par(1:tr.numLabels-1) tr.numLabels]]);
switch orientation
case {'left','right'}
h.BranchLines = plot(X,Y,'-k');
delete(h.BranchLines(~tr.activeNodes))
h.BranchLines = h.BranchLines(tr.activeNodes);
case {'top','bottom'}
h.BranchLines = plot(Y,X,'-k');
delete(h.BranchLines(~tr.activeNodes))
h.BranchLines = h.BranchLines(tr.activeNodes);
end
case 'angular'
X = tr.x([nodeIndex;[tr.par(1:tr.numLabels-1) tr.numLabels]]);
Y = tr.y([nodeIndex;[tr.par(1:tr.numLabels-1) tr.numLabels]]);
switch orientation
case {'left','right'}
h.BranchLines = plot(X,Y,'-k');
delete(h.BranchLines(~tr.activeNodes))
h.BranchLines = h.BranchLines(tr.activeNodes);
case {'top','bottom'}
h.BranchLines = plot(Y,X,'-k');
delete(h.BranchLines(~tr.activeNodes))
h.BranchLines = h.BranchLines(tr.activeNodes);
end
case 'radial'
R = tr.x;
A = tr.y / numel(tr.terminalNodes)*2*pi+rotation*pi/180;
tr.x = R .* sin(A);
tr.y = R .* cos(A);
X = tr.x([nodeIndex;[tr.par(1:tr.numLabels-1) tr.numLabels]]);
Y = tr.y([nodeIndex;[tr.par(1:tr.numLabels-1) tr.numLabels]]);
h.BranchLines = plot(X,Y,'-k');
delete(h.BranchLines(~tr.activeNodes))
h.BranchLines = h.BranchLines(tr.activeNodes);
end
% drawing nodes
switch renderType
case {'square','angular'}
switch orientation
case {'left','right'}
h.BranchDots = plot(tr.x(branchIndex(tr.activeNodes(branchIndex))),...
tr.y(branchIndex(tr.activeNodes(branchIndex))),'o',...
'MarkerSize',5,'MarkerEdgeColor','k',...
'MarkerFaceColor','b');
h.LeafDots = plot(tr.x(leafIndex(tr.activeNodes(leafIndex))),...
tr.y(leafIndex(tr.activeNodes(leafIndex))),'square',...
'MarkerSize',4,'MarkerEdgeColor','k',...
'MarkerFaceColor','w');
case {'top','bottom'}
h.BranchDots = plot(tr.y(branchIndex(tr.activeNodes(branchIndex))),...
tr.x(branchIndex(tr.activeNodes(branchIndex))),'o',...
'MarkerSize',5,'MarkerEdgeColor','k',...
'MarkerFaceColor','b');
h.LeafDots = plot(tr.y(leafIndex(tr.activeNodes(leafIndex))),...
tr.x(leafIndex(tr.activeNodes(leafIndex))),'square',...
'MarkerSize',4,'MarkerEdgeColor','k',...
'MarkerFaceColor','w');
end
case 'radial'
h.BranchDots = plot(tr.x(branchIndex(tr.activeNodes(branchIndex))),...
tr.y(branchIndex(tr.activeNodes(branchIndex))),'o',...
'MarkerSize',5,'MarkerEdgeColor','k',...
'MarkerFaceColor','b');
h.LeafDots = plot(tr.x(leafIndex(tr.activeNodes(leafIndex))),...
tr.y(leafIndex(tr.activeNodes(leafIndex))),'square',...
'MarkerSize',4,'MarkerEdgeColor','k',...
'MarkerFaceColor','w');
end
% resize figure if needed
switch renderType
case {'square','angular'}
switch orientation
case {'left','right'}
correctFigureSize(fig, 15 * numel(tr.terminalNodes),0);
fontRatio = max(get(fig,'Position').*[0 0 0 1])/numel(tr.terminalNodes);
case {'top','bottom'}
correctFigureSize(fig, 0, 15 * numel(tr.terminalNodes));
fontRatio = max(get(fig,'Position').*[0 0 1 0])/numel(tr.terminalNodes);
end
case 'radial'
temp = 10/pi*numel(tr.terminalNodes);
correctFigureSize(fig,temp,temp);
fontRatio = max(get(fig,'Position').*[0 0 1 0])/numel(tr.terminalNodes);
end
set(h.axes,'Fontsize',min(9,ceil(fontRatio/1.5)));
% set branch node labels
X = tr.x(branchIndex(tr.activeNodes(tr.numLeaves+1:tr.numLabels)));
Y = tr.y(branchIndex(tr.activeNodes(tr.numLeaves+1:tr.numLabels)));
switch renderType
case {'square','angular'}
switch orientation
case {'left'}
h.branchNodeLabels = text(X+sepUnit(1)/2,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,'horizontal','right')
set(h.branchNodeLabels,'Fontsize',min(8,ceil(fontRatio/2)));
case {'right'}
h.branchNodeLabels = text(X+sepUnit(1)/2,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/2)));
case {'top'}
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)));
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)