netgraph_draw.m

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

%netgraph_draw(network,varargin)
%
%varargin contains overriding graphics parameters, either as a structure or as a list
%
%parameters:
%
%linecolor FontSize text_offset
%
%arrowstyle   {'fluxes','directions','none'}
%arrowvaluesmax
%
%metstyle     {'box','box_std','none'}
%metcolstyle  {'fixed','values'}
%metvaluesmax
%
%actstyle     {'box','box_std','none'}
%actcolstyle  {'fixed','values'}
%actvaluesmax
%chop_names   (length)

function  network = netgraph_draw(network,varargin)

 black_and_white = 0;
%black_and_white = 1;

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

if length(varargin)
if isstruct(varargin{1}),
  fn = fieldnames(varargin{1});
  for i=1:length(fn), p=setfield( p, fn{i},getfield(varargin{1},fn{i})); end
else
  for i=1:length(varargin)/2, p=setfield( p, varargin{2*(i-1)+1},varargin{2*i}); end
end
end

if ~isfield(p,'metvalues_std'),  p.metvalues_std = zeros(size(p.metvalues));  end; 
if ~isfield(p,'actvalues_std'),  p.actvalues_std = zeros(size(p.actvalues)); end;

if isfield(p,'metabolite_mapping'),
if length(p.metvalues) < length(p.metnames), p.metvalues=p.metvalues(p.metabolite_mapping); end
if length(p.metvalues_std) < length(p.metnames), p.metvalues_std=p.metvalues_std(p.metabolite_mapping);
end
end

if ~isfield(p,'show_regulation'), p.show_regulation=0; end
% values must be normalised
if ~isfield(p,'metvaluesmax'), p.metvaluesmax=[]; end
if ~isfield(p,'actvaluesmax'), p.actvaluesmax=[]; end
if ~isfield(p,'arrowvaluesmax'), p.arrowvaluesmax=[]; end
if isempty(p.metvaluesmax), p.metvaluesmax=max(10^-10,max(abs(p.metvalues))); end
metvalues = p.metvalues /p.metvaluesmax; 
metvalues(find(metvalues>1))=1;  metvalues(find(metvalues<-1))=-1;
metvalues_std =  p.metvalues_std /p.metvaluesmax;
if isempty(p.actvaluesmax), p.actvaluesmax=max(10^-10,max(abs(p.actvalues))); end
actvalues = p.actvalues /p.actvaluesmax; 
 actvalues(find(actvalues>1))=1;  actvalues(find(actvalues<-1))=-1;
  actvalues_std =  p.actvalues_std /p.actvaluesmax;
  if isempty(p.arrowvaluesmax), p.arrowvaluesmax=max(10^-10,max(abs(p.arrowvalues))); end
 arrowvalues = p.arrowvalues /p.arrowvaluesmax; 
 arrowvalues(find(arrowvalues>1))=1;  arrowvalues(find(arrowvalues<-1))=-1; 
 
 if isfield(p,'FontSize'),  fontsize=p.FontSize;
 else, fontsize=8; end

m = p.m;
x = p.x;

n_met=length(metvalues);
n_act=length(actvalues);

plot(x(1,:), x(2,:), 'r.');

axis([-0.1 1.1 -0.1 1.1])
axis equal

[i,j]=find(triu(m)); 
if isfield(p,'linecolor'), linecolor = p.linecolor;
else                       linecolor = [0 0 1];
end
line([x(1,i); x(1,j)],[x(2,i); x(2,j)],'color',linecolor);
hold on

if isfield(p,'m_regulation') & p.show_regulation,
  [i,j]=find(triu(p.m_regulation)); 
  if isfield(p,'linecolor'), linecolor = 0.5+0.5*p.linecolor;
  else                       linecolor = [0. 1 0.];
  end
  line([x(1,i); x(1,j)],[x(2,i); x(2,j)],'color',linecolor);
end


[i1,j1] = find(m(1:n_met,end-n_act+1:end));

switch p.arrowstyle,
  
  case 'fluxes'
   for k=1:length(i), 
     scale = arrowvalues( j1(k) );
      plot_triangle(x(1,i1(k)), x(1,j1(k)+n_met), x(2,i1(k)), x(2,j1(k)+n_met),...
		    p.arrowsize*abs(scale), 'b', -p.N(i1(k),j1(k))*sign(scale)); 
   end
   
  case 'directions'
    for k=1:length(i1), 
      plot_triangle(x(1,i1(k)), x(1,j1(k)+n_met), x(2,i1(k)), x(2,j1(k)+n_met),...
		    p.arrowsize, 'b', -sign(p.N(i1(k),j1(k)))); 
    end
    
end

if black_and_white, 
  d = 0.5-0.5*sign(gray(250)-0.5);
else,
  d = my_colors;
end

switch p.metcolstyle
  case 'fixed',  c = repmat(p.metcol,n_met,1);
  case 'values',  c=d(ceil(1+(1+metvalues)*0.5*249),:);
end

switch p.metstyle
 case 'box',
  for i=1:n_met,  plot_octagon(x(1,i),x(2,i),abs(metvalues(i)),0*metvalues_std(i),p.squaresize,c(i,:)); end; 
 case 'box_std',
  for i=1:n_met,  plot_octagon(x(1,i),x(2,i),abs(metvalues(i)),metvalues_std(i),p.squaresize,c(i,:)); end; 
end

switch p.actcolstyle
   case 'fixed',  c = repmat(p.actcol,n_act,1);
  case 'values',  c=d(ceil(1+(1+actvalues)*0.5*249),:);
end

switch p.actstyle,
 case 'box',
  for i=1:n_act,    plot_square(x(1,i+n_met),x(2,i+n_met),abs(actvalues(i)),0*actvalues_std(i),p.squaresize,c(i,:)); end; 
 case 'box_std',
  for i=1:n_act,    plot_square(x(1,i+n_met),x(2,i+n_met),abs(actvalues(i)),actvalues_std(i),p.squaresize,c(i,:)); end; 

end

hold off

if isfield(p,'chop_names'),
    dummi = char(p.metnames);
    p.metnames=cellstr(dummi(:,1:min(p.chop_names,size(dummi,2))));
    dummi = char(p.actnames);
    p.actnames=cellstr(dummi(:,1:min(p.chop_names,size(dummi,2))));
end

if isfield(p,'text_offset'), text_offset=p.text_offset; else text_offset=[0;-0.01]; end

if p.metprintnames, text(x(1,1:n_met) + 0.5*p.squaresize*(0.5+sqrt(abs(metvalues)'+ metvalues_std')) +text_offset(1),x(2,1:n_met)+text_offset(2), p.metnames,'FontSize',fontsize); end
if p.actprintnames, text(x(1,n_met+1:end) + 0.5*p.squaresize*(0.5+sqrt(abs(actvalues)'+actvalues_std')) +text_offset(1),x(2,n_met+1:end)+text_offset(2), p.actnames,'FontSize',fontsize); end

if p.metprintvalues, 
 if find(p.metvalues_std~=0), 
   strings =  [num2str(p.metvalues,3) repmat(' \pm ',n_met,1) num2str(p.metvalues_std,2)];
 else 
   strings = num2str(p.metvalues_std); 
 end
 offset=0.5*p.squaresize*(0.5+sqrt(abs(metvalues)'+metvalues_std'));
 text(x(1,1:n_met)+0*offset,x(2,1:n_met)+ offset,strings,'FontSize',fontsize); 
end

if p.actprintvalues, 
  if find(p.actvalues_std~=0),
  strings =  [num2str(p.actvalues,3) repmat(' \pm ',n_act,1) num2str(p.actvalues_std,2)];
 else strings = num2str(p.actvalues); end
offset=0.5*p.squaresize*(0.5+sqrt(abs(actvalues)'+actvalues_std'));
text(x(1,n_met+1:end) + 0*offset,x(2,n_met+1:end) + offset,strings,'FontSize',fontsize); 
end

network.graphics_par = p;

noticks


% -----------------------------------------------------

function plot_square(x,y,l,std,squaresize,col)

l_max = squaresize*sqrt(l+std); l_min = squaresize*sqrt(max(0,l));
fill(x + 0.5 * l_max*[-1 1 1 -1], y + 0.5*l_max*[-1 -1 1 1],1+0*col)
fill(x + 0.5 * l_min*[-1 1 1 -1], y + 0.5*l_min*[-1 -1 1 1],col)


function plot_octagon(x,y,l,std,squaresize,col)

l_max = squaresize*sqrt(l+std); l_min = squaresize*sqrt(max(0,l));
fill(x + 0.5 * l_max * 4/pi* [-1 -0.5 0.5 1 1 0.5 -0.5 -1], y + 0.5*l_max*4/pi*[-0.5 -1 -1 -0.5 0.5 1 1 0.5],1+0*col)
fill(x + 0.5 * l_min * 4/pi* [-1 -0.5 0.5 1 1 0.5 -0.5 -1], y + 0.5*l_min*4/pi*[-0.5 -1 -1 -0.5 0.5 1 1 0.5],col)

function plot_triangle(xmin, xmax, ymin, ymax, l, col,reverse)

phi = angle( xmax-xmin + i *(ymax-ymin));
 points = repmat([xmin; ymin] + 0.5*[xmax-xmin; ymax-ymin],1,3) ...
	  + reverse * [cos(phi) -sin(phi); sin(phi) cos(phi)] * l * [0 1 0; -0.3 0 0.3];
 fill(points(1,:),points(2,:),col)