Hello!
I have a gene coexpression network and i want to analyse and visualize the clusters of the network (i.e show different clusters in different colours). I have used R studio and cytoscape for the network construction and analysis, so far. Although i have managed to define the modules of the network with different algorithms, i couldn't find a proper way to visualize the clusters. Cytoscape plugins Glay and ClusterMaker seemed very helpful but unfortunately they are not compatible with cytoscape 2.8.
Could you recommend similar cytoscape plugins, r packages and/or any other software for this kind of analysis?
Thanks in advance, Ane
•
written
by
Ane •
2 answers
I'm using ClusterMaker with Cytoscape 2.8 without problem. Once you have created the cluster, a button appears allowing you to visualize them.
The answer comes quite late, but maybe it still can be useful for someone. When you create the clusters, there is an advanced Cytoscape option to generate metanodes. An attribute will be added to each node that you can use to colour the clusters.
Log in to answer this question.
-
network visualization (multiple data source integration)
written by lessismore
-
What does cluster number in ClusterMaker represent?
written by Arindam Ghosh
-
What if a network is not scale-free?
written by Arindam Ghosh
-
how to visulaize WGCNA network file in cytoscape
written by Azhar •
-
Plotting large PPI biological networks
written by beingseema03 •
-
What data should I use to generate a gene coexpression network?
written by tahermun •
-
Gene Network construction
written by alpha09 •
-
Bayesian Network from R to visualize in cytoscape
written by Maria •
-
Rna-Seq Rpkm For Coexression By Wgcna
written by l0o0
-
Microarray Expression Data For Network Analysis
written by pixie@bioinfo
"used R studio" - Rstudio is an R IDE, so this does not tell us what you did. Did you use an R package?
yes, i used igraph and i have imported it into cytoscape with graphml plugin