netgraph_make_graph.m

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

% network = netgraph_make_graph(network,metvalues,actvalues);
%
% create or modify structure describing the graphical appearance of a metabolic network

function network = netgraph_make_graph(network,metvalues,actvalues);

gridsize = 0.01; % distance between discrete x values
k1 = 0.1;  % overall repulsion strength
k2 = 0.01;  % overall repulsion scale
k3 = 0.5;  % neighbour attraction strength
k4 = 0.1;  % neighbour attraction scale

if ~exist('metvalues','var'),  metvalues = -ones(length(network.metabolites),1); end
if ~exist('actvalues','var'),  actvalues = ones(length(network.actions),1);     end

% metnames = break_names(network.metabolites);
% actnames = break_names(network.actions);

metnames = strrep(network.metabolites,'_',' ');
actnames = strrep(network.actions,'_',' ');
metnames = strrep(metnames,'Compartment ','');
metnames = strrep(metnames,'Cell ','');
metnames = strrep(metnames,'Compound ','');
metnames = strrep(metnames,'Enzyme ','');
metnames = strrep(metnames,'PseudoBioObj ','');
metnames = strrep(metnames,'  ',' ');
actnames = strrep(actnames,'PseudoBioObj.','');
actnames = strrep(actnames,'Enzyme.','');

graphics_object.metvalues      = metvalues; 
graphics_object.actvalues      = actvalues;
graphics_object.arrowvalues    = actvalues;
% if ~isfield(graphics_object,'metvalues_std'), graphics_object.metvalues_std  = 0*metvalues; end
% if ~isfield(graphics_object,'actvalues_std'), graphics_object.actvalues_std  = 0*actvalues; end

graphics_object.metstyle       = 'box'; % , 'box', 'diamond', 'none'
graphics_object.metcolstyle    = 'values'; % 'fixed'
graphics_object.metcol         = 'c';  % used if metcolstyle ==  'fixed'
graphics_object.metprintnames  = 1;
graphics_object.metprintvalues = 0;
graphics_object.metnames       = metnames;

graphics_object.actstyle       = 'box'; % , 'box', 'diamond' 'none'
graphics_object.actcolstyle    = 'values'; % 'fixed'
graphics_object.actcol         = 'r'; % used if actcolstyle ==  'fixed'
graphics_object.actprintnames  = 1;
graphics_object.actprintvalues = 0;
graphics_object.actnames       = actnames;

graphics_object.arrowstyle     = 'directions';  % 'fluxes', 'none'

graphics_object.squaresize     = 0.2/sqrt(length(metnames));
graphics_object.arrowsize      = 0.08/sqrt(length(metnames));
graphics_object.lambda         = 1;
graphics_object.N              = network.N;

graphics_object.metabolite_mapping = (1:length(metnames))';

% adjacency matrix between metabolites and reactions 
m = [zeros(length(network.metabolites)) network.N; network.N' zeros(length(network.actions))];
m = (m~=0);
m = m-diag(diag(m));
db = graph_shortest_path(m,4,0);
db(find(~isfinite(db)))=5; 

if isfield(network,'regulation_matrix'), 
  graphics_object.m_regulation = [zeros(length(network.metabolites)) network.regulation_matrix'; network.regulation_matrix zeros(length(network.actions))];
end


graphics_object.m  = m;
graphics_object.db = db;

% --- calculate graph node positions x

x = netgraph_find_x(graphics_object,gridsize,k1,k2,k3,k4);
graphics_object.x = x;

graphics_object.fixed = zeros(size(x,2),1);

network.graphics_par = graphics_object;