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nolanlab / vortex

VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
https://github.com/nolanlab/vortex/releases
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Possible to export minimum spanning tree cluster x-y coordinates? #5

Open Andrew-InTheBox opened 7 years ago

Andrew-InTheBox commented 7 years ago

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 commented 6 years ago

@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 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 notifications@github.com 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....

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Andrew-InTheBox commented 6 years ago

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 commented 6 years ago

Aah, OK sorry yes - let me add it then On Mon, Oct 23, 2017 at 11:49 AM Andrew Box notifications@github.com 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.

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Andrew-InTheBox commented 6 years ago

That's excellent @nsamusik , thanks!