I wonder if i could use cytoscape for genie3(gene regulatory network) result for visualization of the interaction among the input genes.
The result file was in the csv format, the major challenge for me was the selection of the best informative interaction (or the gene with highest number of interaction )as the file include 19k interaction when run cytoscape the interaction ////////////////////
This is the codes that I run. Is there any parameter that I should include
library(GENIE3) library(igraph) library(RCy3) library(Rgraphviz) expr_data <- as.matrix(read.table("upanddowngene.csv", header = T, sep = ",",row.names = 1)) set.seed(expr_data) weightMat <- GENIE3(expr_data) linkList <- getLinkList(weightMat) edge_listsi <- linkList Gsi <- graph.data.frame(edge_listsi,directed = F) Asi <- get.adjacency(Gsi,sparse = F,attr = "weight",type = "both") g_arasi <- graph.adjacency(Asi,mode = "undirected",weighted = T) g.cyto <- igraph.to.graphNEL(g_arasi) cw = createNetworkFromGraph("net", graph=g.cyto) displayGraph (cw)