netgraph_move.m

％The Metabolic Networks Toolbox contains functions to create, ％modify, display, and simulate bioche

function network = netgraph_move(network,flag_draw_details)

%network = netgraph_move(network,flag_draw_details)
%
%move nodes of metabolic network graph with the mouse
%
% left button:     first click: choose node
%                 second click: choose new position
% center button:   relax positions
% right button:    quit
%
% flag_draw_details (optional): 0: only reaction lines
% 1: also regulation lines
% 2: also node names

fprintf('Left button  : choose node to move. Place it with the left button (free position) or center button (fixed position)\nCenter button: Relax the network\nRight button : Quit\n');

if ~isfield(network,'graphics_par'),
  network=netgraph_make_graph(network);
end

gridsize = 0.01; % distance between discrete x values
k1 = 0.01;  % overall repulsion strength
k2 = 0.5*sqrt(1/length(network.graphics_par.metnames));  % overall repulsion scale
k3 = 0.2;  % neighbour attraction strength

if ~exist('flag_draw_details','var'), flag_draw_details = 0;  end;
if ~isfield(network.graphics_par,'fixed'), network.graphics_par.fixed = zeros(size(network.graphics_par.x,2),1); end

p   = network.graphics_par;
db  = network.graphics_par.db;
m   = network.graphics_par.m;
x   = network.graphics_par.x;
p.x = x;
names=[network.graphics_par.metnames; network.graphics_par.actnames];

p.arrowstyle='none';
switch flag_draw_details,
 case 0, netgraph_draw_simple(network); noticks;
 case 1, netgraph_draw_simple(network,1); noticks;
 case 2, netgraph_draw(network,p); noticks;
end

% noticks;

cont = 1;

[Ni,Nj]=ind2sub(size(p.N),find((p.N~=0)));
Nj = Nj+length(p.metnames);
  edgecenters = 0.5*(x(:,Ni)+x(:,Nj));
   hold on;      %     plot(edgecenters(1,:),edgecenters(2,:),'g.');
     fixed = find(network.graphics_par.fixed);
     plot(network.graphics_par.x(1,fixed),network.graphics_par.x(2,fixed),'k.');
     hold off;

while cont==1,

     [x_old,y_old,button] = ginput(1);
     dist= sum( (repmat([x_old;y_old],1,size(x,2))-x).^2);
     [dum,i]=min(dist);
     index=i(1);
     loose=find(1-network.graphics_par.fixed);
     switch button
       case 1,
	 loose=find(1-network.graphics_par.fixed);
	 [x_new,y_new,button] = ginput(1);
	 factors = exp(-network.graphics_par.db(index,:)/network.graphics_par.lambda);
	 x(:,loose) = x(:,loose) + [x_new-x_old; y_new-y_old] * factors(:,loose);
         network.graphics_par.fixed(index) = button-1;
       case 2,
	 x = x + 0.001*randn(size(x));
	 for it=1:3
	   edgecenters = 0.5*(x(:,Ni)+x(:,Nj));
	   for i=1:size(x,2);
	     distances = repmat(x(:,i),1,size(x,2)+length(Ni)) - [x, edgecenters]; %
             f1 = sum(distances.^2)+10^-10;
	     f1 = exp(-f1/(2*k2^2))./sqrt(f1);
             dummy = x(:,find(db(i,:)==1));
	     if length(dummy),	       xdum = mean(dummy,2);
	     else,                     xdum = x(:,i);	       end
	       xnew(:,i)= x(:,i) + k1 * sum(distances.*repmat(f1,2,1),2) ...
		   + k3 * ( xdum - x(:,i) );
	   end
	   loose=find(1-network.graphics_par.fixed);
	   if length(loose),
	     x(:,loose) = xnew(:,loose);
	     x(:,loose) = x(:,loose)-repmat(min(x(:,loose)')',1,size(x(:,loose),2));
	     x(:,loose) = diag(1./(max(x(:,loose)')'))*x(:,loose);
	     x(:,loose) = gridsize * round(x(:,loose)/gridsize);
	   end
	 end
       case 3,
	 cont = 0; 
     end
     
     loose = find(1-network.graphics_par.fixed);
     if length(loose),
       x(:,loose) = x(:,loose)-repmat(min(x(:,loose)')',1,size(x(:,loose),2));
       x(:,loose) = diag(min(1,1./(max(x(:,loose)')')))*x(:,loose);
       x(:,loose) = gridsize * round(x(:,loose)/gridsize);
     end
     network.graphics_par.x = x;
     edgecenters = 0.5*(network.graphics_par.x(:,Ni)+network.graphics_par.x(:,Nj));
     
     switch flag_draw_details,
     case 0,      netgraph_draw_simple(network);   noticks;
     case 1,      netgraph_draw_simple(network,1);   noticks;
     case 2,                netgraph_draw(network,network.graphics_par);  noticks;  end

      hold on; %           plot(edgecenters(1,:),edgecenters(2,:),'g.'); 
      fixed = find(network.graphics_par.fixed);
      plot(network.graphics_par.x(1,fixed),network.graphics_par.x(2,fixed),'k.'); hold off
      hold off;
% noticks;
end