create force directed layout gexf file with node position generation - php

Question

In my Database i've got nodes and edges.
Position must have generated at gexf generation, the node must not overlap and
generate this kind of Graph: http://www.nwoods.com/components/images/force-directed-layout.png
I use Sigma.js for presentating the graph.
How can i calculate the node postition with an force directed alogrithm, with a root item?
Or there a layout that can generate from node and edges a layout that not overlap and output like this png above?
EDIT:
PHP code for generating node position:
function _generate_gexf_node($test=false){
$count = 0;
foreach ($node_array as $node) {
$node_size = '22.714287';
$node_poz = ' x="'.rand(10, 300).'" y="'.rand(10, 300).'" z="'.rand(10, 300).'" ';
$node_color = ' b="45" g="72" r="216" ';
$data['node'][] = '<node id="'.$node['node_id'].'" label="'.$node['label'].'">
<attvalues>
<attvalue for="authority" value="0.01880342"/>
<attvalue for="hub" value="0.01880342"/>
</attvalues>
<viz:size value="'.$node_size.'"/>
<viz:color '.$node_color.'/>
<viz:position '.$node_poz.'/>
</node>
';
$count++;
}
return $data;
}
How can i gnerete the position in "runtime", to like this http://www.nwoods.com/components/images/force-directed-layout.png?
Where can i find implementation of YiFan Hu Force directed algorithm?
Or a special Bubble layout implementation?

Answer 1

at the moment i work also on a Web Graph Visualization but with javascript.
Here exists a good project called gexf-js (https://github.com/raphv/gexf-js)
but this is only for drawing the graph.
For the layout stuff i used the gephi library (this is implemented in java)
you can download it here https://gephi.org/toolkit/. And i found also a good example
for the YifanHu layout Algorithm.
If it it could a manual task than you can import your gexf file in the gephi program
runt the layouter you want and export it as gexf. Most of all function in the gephi program
are also available in the toolkit library.
Hopefully this helps
nice day