I have a control vs treated RNA-seq plant data for which I am trying to construct gene co-expression network.
The normalized count matrix of 6000 DEGs idenftifed are derived after rlog transformation was inputted to Cor() function and Pearson correlation was applied. The pair wise correlation analysis gave ~30 million gene pairs out of which, gene pairs were selected with a cutoff >=0.95
In the input file for cytoscape, I notice that there are repetition of node pairs connected through same correlation value. For example
geneA geneB 0.967634
geneB geneC 0.976453
geneB geneA 0.967634
Is it possible to get node connection like this with same correlation value?
If it so should i consider only one pair (geneA geneB 0.967634) and discard the other (geneB geneA 0.967634)?
I'm using Cytoscape for visualizing this gene co-expression network but it is huge. Specifically, it has 11934 nodes and 518282 edges
By default cytoscape is opening the network in "prefuse force directed layout",
Is prefuse force directed layout a directed graph?
Why cytoscape load the network in such a layout?
is there a better way for visualizing my network in Cytoscape?