Added source Matlab code for reference

matlab/graph/viewPhylogeny.m

@@ -0,0 +1,96 @@
+function viewPhylogeny(action)
+% VIEWPHYLOGENY function draws phylogenetic trees
+
+% load the mixture result
+
+warning('off','MATLAB:dispatcher:InexactMatch')
+
+h0 = findobj('Tag','load_menu');
+c = get(h0,'UserData');
+h0 = findobj('Tag','filename1_text');
+filename = get(h0,'String');
+
+aln.npops = c.npops;
+aln.COUNTS = c.COUNTS;
+aln.adjprior = c.adjprior;
+aln.data = c.data;
+aln.partition = c.PARTITION;
+aln.clusternames = ''; % default cluster names are 1 x npops integers.
+aln.noalle = c.noalle;
+clear c;
+
+disp('---------------------------------------------------');
+if strcmp(action, 'nj')
+    disp('Viewing the Neighbor-Joining tree.');
+else
+    disp('Viewing the UPGMA tree.');
+end
+disp(['Load the mixture result from: ',[filename],'...']);
+
+% Select the type of distance matrix
+[D] = chooseDistance(aln);
+if (isempty(D))
+    return;
+else
+    % draw the window
+    h0 = figure('NumberTitle','off');
+    set(h0, 'NumberTitle', 'off');
+    set(h0,'menubar','none','toolbar','figure');
+    set(h0,'Tag','nj_plot');
+    set(h0,'Name',[ upper(action) ' tree - ' filename]);
+    h1 = uimenu('Parent',h0, ...
+        'Label','Attributes', ...
+        'Tag','attr_menu');
+    h2 = uimenu('Parent',h1, ...
+        'Label','Rename clusters', ...
+        'callback', 'plotflow rename', ...
+        'Tag','clustername_menu');
+    h2 = uimenu('Parent',h1, ...
+        'Label','Visual type', ...
+        'Tag','visualtype_menu');
+    h3 = uimenu('Parent',h2, ...
+        'Label','Square', ...
+        'callback', 'viewDendrogram(''square'')', ...
+        'Tag','viewsquare_menu');
+    h3 = uimenu('Parent',h2, ...
+        'Label','Angular', ...
+        'callback', 'viewDendrogram(''angular'')', ...
+        'Tag','viewangular_menu');
+    h3 = uimenu('Parent',h2, ...
+        'Label','Radial', ...
+        'callback', 'viewUnrooted(''radial'')', ...
+        'Tag','viewradial_menu');
+    h3 = uimenu('Parent',h2, ...
+        'Label','Phylogram', ...
+        'callback', 'viewUnrooted(''phylogram'')', ...
+        'Tag','viewphylogram_menu');
+
+    if strcmp(action, 'nj')
+        t = seqNeighJoin(D, 'equivar', correct(aln.clusternames, aln.npops));
+    else
+        t = seqlinkage(D, 'average', correct(aln.clusternames, aln.npops));
+    end
+    Plot(t);
+end
+
+% save the parameters
+% g.handle = h0;
+g.varnames = correct(aln.clusternames, aln.npops);
+g.D = D;
+g.type = action;
+g.filename = filename;
+g.visualtype = 'square';
+g.tree = t;
+set(h1,'Userdata',g); % store in the attribute menu
+
+%--------------------------------------------------------------------------
+% SUBFUNCTIONS
+%--------------------------------------------------------------------------
+function varnames = correct(clusternames,npops)
+
+varnames = cell(1,npops);
+if isempty(clusternames)
+    for i=1:npops
+        varnames{i} = sprintf('Cluster %d',i);
+    end
+end