# NOT RUN {
rm(list = ls())
library(MEGENA)
data(Sample_Expression)
ijw <- calculate.correlation(datExpr[1:100,],doPerm = 2)
el <- calculate.PFN(ijw[,1:3])
g <- graph.data.frame(el,directed = FALSE)
MEGENA.output <- do.MEGENA(g = g,remove.unsig = FALSE,doPar = FALSE,n.perm = 10)
output.summary <- MEGENA.ModuleSummary(MEGENA.output,
mod.pvalue = 0.05,hub.pvalue = 0.05,
min.size = 10,max.size = 5000,
annot.table = NULL,id.col = NULL,symbol.col = NULL,
output.sig = TRUE)
pnet.obj <- plot_module(output = output.summary,PFN = g,subset.module = "comp1_2",
layout = "kamada.kawai",label.hubs.only = FALSE,
gene.set = list("hub.set" = c("CD3E","CD2")),color.code = c("red"),
output.plot = FALSE,out.dir = "modulePlot",col.names = c("grey","grey","grey"),
hubLabel.col = "black",hubLabel.sizeProp = 1,show.topn.hubs = Inf,show.legend = TRUE)
pnet.obj
# }
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