Question: Network modeling of data produced by mixOmics (R) in Cytoscape
0
gravatar for IrK
4 months ago by
IrK40
Australia
IrK40 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 4 months ago by IrK40

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 4 months ago by Jean-Karim Heriche21k

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

ADD REPLYlink written 4 months ago by IrK40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1892 users visited in the last hour