Cytoscape Layouts

[pine...@gmail.com]

Hi I am new to Cytoscape and I would like to know if there is a way to import or select other layouts that are not apart of the default layouts. I need to put my networks into the Fruchterman Reingold, Force Atlas, and the Multidimensional Scaling layouts/ algorithms. Thank you.

[Scooter Morris]

On 6/20/17 12:34 PM, pine...@gmail.com wrote:
> Hi I am new to Cytoscape and I would like to know if there is a way to import or select other layouts that are not apart of the default layouts. I need to put my networks into the Fruchterman Reingold, Force Atlas, and the Multidimensional Scaling layouts/ algorithms. Thank you.
>

Greetings,

Well, "biolayout" is one of the standard layouts and it actually
implements Fruchterman-Reingold. A variant of MDS is available in
clusterMaker2 -- look at the PCoA algorithm. Don't know about Force
Atlas, though.


-- scooter

[Nate Pines]

Thank you! What about t-SNE? Is there a layout in Cytoscape 3.5.1 for this layout/ algorithm.

-- scooter


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[Scooter Morris]

On 6/21/17 9:25 AM, Nate Pines wrote:

Thank you! What about t-SNE? Is there a layout in Cytoscape 3.5.1 for this layout/ algorithm.

Yes -- I just added t-SNE to clusterMaker2 last month.  You'll need to run t-SNE, bring up the plot, and then you can map the coordinates to the network view.

-- scooter

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