97 lines
2.8 KiB
Mathematica
97 lines
2.8 KiB
Mathematica
|
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
|