Graph Layouts

[Rob Anderson]

Hi all,

Let me first thank you guys for building a solid tool that I quite enjoy using.  

I've noticed, as others have, that the ForceDirected layout is based on a simulation that has a random seed and is not guaranteed to draw the same way each time.  

Are the circle and radial layouts built in the same way?  

Would it be possible in a future version to expose an API method like "setRandSeed(int)" such that we can force the simulation to play out the same way and return the same graph?  Perhaps at least for testing purposes? 

[Christian Tannus Lopes]

No, Circle and Radial layouts are deterministic.

We will add your feature request for allowing the client app to set the seed to out list.

Thanks.

[Max Franz]

It may be a simpler alternative to just have a `deterministic` flag option.  If enabled, it would use some predefined seed.  This avoids having the user needing to specify a seed himself.  It's good enough if the user just wants the graph to look the same each time, even though specifying the seed manually is more flexible.

[Quaid Morris]

Having a method to set the random is a very standard solution to these type of problem and would be something users would expect. Then it would be trivial to also have a deterministic flag.

[Rob Anderson]

Thanks for your quick feedback!  

I was able to look deeper into the theory behind the ForceDirected graph and I now understand why it's not deterministic.  

For now, I'm going to implement a method to define my nodes with XGMML and set positions either manually or with a 3rd party Java library.  I believe I've found several open source options for this, but does anyone have any favorites or recommendations?

Cheers,

Rob

[Naveed]

On Nov 1, 2:12 pm, Christian Tannus Lopes <chrtan...@gmail.com> wrote:
> No, Circle and Radial layouts are deterministic.
> We will add your feature request for allowing the client app to set the seed to out list.
>
> Thanks.

Christian, I am REALLY looking forward to this feature that will allow
you to seed the force directed algorithm :) Any idea when it will be
available?
-Naveed

[Christian Tannus Lopes]

Hi Naveed,

I can't give you a date but will try to implement it for the next release.

You can follow it here: http://cbio.mskcc.org/cytoscape/bugs/view.php?id=2611

Thanks,

Christian

[sateesh kumar]

Hi, I also trying to get the Force-directed graph in cytoscapeweb... but i didn't get any information how to do?