Layout help

[abhishake lahiri]

Hello,

I came across this figure in a paper "Chen, Casey, et al. "Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy." The ISME journal 12.5 (2018): 1210." and have been trying to make a similar result using my own data. However, my knowledge in layouts is not extensive enough. Can anyone please help me obtaining a similar structure of the network. Basically I want to keep the nodes in a similar filled up circular manner. Here the colors are the module numbers of those nodes.

Thanks in advance,

Abhishake.  

[Kei]

I’m not sure this creates simillar result for smaller networks or not, but this image was created with Cytoscape:

http://cytoscape.org/images/screenshots/structure-aware-layout.jpg

With this script via CyRest and R.

https://github.com/idekerlab/cy-rest-R/blob/develop/workflow1_structure_based_visualization.R

Maybe worth trying to use your data?

Kei

[piet molenaar]

Hi,

In addition to Kei's remarks, this looks to me as an voronoi distribution of points over a circle; I'm not aware of a layout currently available in Cytoscape that can produce such a layout.

However, if you have access to the scripts producing the random matrix theory (RMT)-based layout (as described in the article) in x and y coordinates you can load these as node attributes and base the layout on these.

Best,

Piet

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Amsterdam University Medical Centers 
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

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