Added source Matlab code for reference

matlab/graph/graphvis2.m

@@ -0,0 +1,108 @@
+function graphvis2(adj_mat, linkage_file_name, inliers, graphviz_path, npops)
+% Filename: graphvis2.m
+% graphvis2(adj_mat, linkage_file_name)
+%
+% Description: 
+% Graph visualization given the adjacency matrix. 
+
+% Author: Jing Tang
+% Modified date: 01/06/2005
+
+% Input:
+% adj_mat: The adjacency matrix.
+% linkage_file_name:
+
+% Output:
+%
+
+% Ensure adj_mat is symmetric and square.
+
+[n,m] = size(adj_mat);
+if n ~= m, error ('Adjacency matrix must be square'), end;
+%if ~all(diag(adj_mat)), error('The diagonal must be nonzero'), end;
+
+npops_in = length(inliers);
+groupnames = cell(1,npops_in);
+nodecolors = cell(npops_in,1);
+allnode_color = giveColors(npops);
+arccolors = cell(npops_in);
+adjmat = adj_mat ~= 0;
+for i=1:npops_in
+    groupnames{i} = sprintf('Cluster %d',inliers(i));
+    nodecolors{i} = num2str(rgb2hsv(allnode_color(inliers(i),:)));
+    arccolors(i,adjmat(i,:)) = {nodecolors{i}};
+end
+nodestyles = cell(npops_in, 1);
+nodestyles(:) = {'filled'};
+arcstyles = cell(npops_in);
+arcstyles(adjmat) = {'filled'};
+
+handle = plotmodel(adj_mat',[1:npops_in],'graphvizpath', graphviz_path, ...
+                             'nodecolors', nodecolors, ...
+                             'nodestyles', nodestyles, ...
+                             'arccolors',arccolors, ...
+                             'arcstyles',arcstyles, ...
+                             'varnames', groupnames);
+
+% set(handle,'menubar','none','numbertitle','off','toolbar','figure');
+set(handle,'numbertitle','off','toolbar','figure');
+m = findall(gcf,'type','uimenu');
+set(m([1:7]),'Visible', 'off');
+
+h1 = uimenu('Parent',handle, ...
+    'Label','Attributes', ...
+    'Tag','attr_menu');
+h2 = uimenu('Parent',h1, ...
+    'Label','Rename clusters', ...
+    'callback', 'plotflow rename', ...
+    'Tag','clustername_menu');
+h3 = uimenu('Parent',h1, ...
+    'Label','Prune edges', ...
+    'callback','plotflow prune', ...
+    'Tag','edge_menu');
+h4 = uimenu('Parent',handle, ...
+    'Label','Help', ...
+    'callback', 'plotflow help', ...
+    'Tag','help_menu');
+% h5 = uimenu('Parent',h1, ...
+%     'Callback','baps4cbf about', ...
+%     'Enable','on', ...
+%     'Label','About', ...
+%     'Tag','about_menu');
+set(handle,'Name',[' Gene flow - ' linkage_file_name ]);
+
+% save the parameters
+g.handle = handle;
+g.adjmat = adj_mat';
+g.adjmat2 = g.adjmat;
+g.k = [1:npops_in];
+g.graphvizpath = graphviz_path;
+g.nodecolors = nodecolors;
+g.nodestyles = nodestyles;
+g.arccolors = arccolors;
+g.arcstyles = arcstyles;
+g.varnames = groupnames;
+g.type = 'GENEFLOW';
+set(h1,'Userdata',g); % store in the attribute menu
+
+
+
+% Old version 
+
+% Decide the coordinate of each node.
+% [p,p,r] = dmperm(adj_mat);
+% nnodes = length(adj_mat);
+% nblocks = length(r)-1;
+% [B,ix]=sort(p,2);
+% Coordinates=[[ix'],zeros(nnodes,1)];
+% 
+% % Plot the graph structure
+% clf reset
+% set(gcf, 'color', 'white', 'menubar', 'none', 'numbertitle','off','name', 'Graphical model')
+% gplot(adj_mat, Coordinates, '-ob');
+% h=findobj(gca, 'type','line');
+% set(h,'markersize',10) 
+% xlim([0 nnodes+1]);
+% axis off
+% text(Coordinates(:,1),Coordinates(:,2)-0.1, int2str(B(:)));
+%drawnow