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