Question: Network modeling of data produced by mixOmics (R) in Cytoscape
gravatar for IrK
14 months ago by
IrK50 wrote:

Hey guys,

I'd like to visualize a network / relationships between two types of data(transcriptome data vs promote data) The network() function (Relevance Network) of the mixOmics R package suggests to save results as the graph object that can be used by Cytoscape to improve visualization. I've check the Cytoscape Apps, and couldn't find any relevant plug-ins. Omics Visualizer - is not relevant to this task.
OmicsAnalyzer - doesn't have valid instructions (The requested URL /~jlv/omicsanalyzer/OmicsAnalyzer_Tutorial_Data_Import.pdf was not found on this server.)

Just wondering if there is a Cytoscape plug-ins that helps to improve visualization generated by mixOmics (R)? Or maybe any other way of visualizing multi omics datasets generated by mixOmics ?

Would appreciate any suggestions.

thank you.

ADD COMMENTlink written 14 months ago by IrK50

It seems to me that you could simply use base Cytoscape to start with. Also since you're already in R, why not use the igraph package which I believe is already required/used by mixOmics. See this tutorial on graph visualization in R.

ADD REPLYlink written 14 months ago by Jean-Karim Heriche23k

I found the igraph tutorial today, will try it out :) thanks for the prompt reply.

ADD REPLYlink written 14 months ago by IrK50
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