Possible to export minimum spanning tree cluster x-y coordinates?

[Andrew-InTheBox]

The ability to export minimum spanning tree cluster spatial coordinates along with event would be useful for doing analysis and gating on the spanning tree in 3rd party applications. Similar to the 'export cell coordinates' option for the force directed layouts.

[malcook]

@AndyinMission - Barring the addition of such a capability to vortex, knowing your an R adept, I recommend you re-layout the vortex clusters in R using igraph's force directed layout, which will probably yield results most similar to the org.gephi.layout.plugin.forceAtlas2.ForceAtlas2 used in this project, and from which you can obtain the graphical coordinates to feed to your 3rd party application.

[Andrew-InTheBox]

Thanks @malcook . But it's actually the minimum spanning tree functionality that I want to export node coordinates for. The force directed layout already allows this straight from vortex.

[malcook]

Perhaps re-do both the MST and the layout??? The MST part should be deterministic, so the result should be the same as Vortex' version....

[nsamusik]

Have you tried exporting it as GraphML and then redoing the layout in Gephi or Cytoscape or R? Let me know if this might work Nikolay

On Mon, Oct 23, 2017 at 11:36 AM Malcolm Cook ***@***.***> wrote: Perhaps re-do both the MST and the layout??? The MST part should be deterministic, so the result should be the same as Vortex' version.... — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADacL6ZFZMYEzO4fI54tfzF9o1MdDoowks5svNyugaJpZM4NubnU> .

-- Nikolay

…

---------------------------------------------------------------------------- This message is intended for the named addressee(s) only. It may contain privileged and confidential information and protected by a copyright. Any disclosure, copying or distribution of this message is prohibited and may be unlawful. If you are not the intended recipient, please destroy this message and notify me immediately. Thank you for your cooperation.

[Andrew-InTheBox]

Thanks @nsamusik , however I'm not seeing 'export as graphML' option for the MST, only for the force directed graphs. MST graphing only shows 'export images' and 'save as pdf' options.

[nsamusik]

Aah, OK sorry yes - let me add it then

On Mon, Oct 23, 2017 at 11:49 AM Andrew Box ***@***.***> wrote: Thanks @nsamusik <https://github.com/nsamusik> , however I'm not seeing 'export as graphML' option for the MST, only for the force directed graphs. MST graphing only shows 'export images' and 'save as pdf' options. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADacLw0lGUuZmGrvzlRP3yqOPvaHwQy4ks5svN-5gaJpZM4NubnU> .

-- Nikolay

…

---------------------------------------------------------------------------- This message is intended for the named addressee(s) only. It may contain privileged and confidential information and protected by a copyright. Any disclosure, copying or distribution of this message is prohibited and may be unlawful. If you are not the intended recipient, please destroy this message and notify me immediately. Thank you for your cooperation.

[Andrew-InTheBox]

That's excellent @nsamusik , thanks!