cy3Network: visualize the network by Cy3

In jianhong/GeneNetworkBuilder: GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

visualize the network by Cy3

Description

Using RCy3 to visualize the network.

Usage

cy3Network(
  gR = graphNEL(),
  ...,
  stringify = FALSE,
  species = "Homo sapiens",
  style = "Marquee",
  widths = c(0.25, 5)
)

Arguments

gR	an object of graphNEL
...	parameters will be passed to createNetworkFromGraph
stringify	Run STRINGify or not
species	if stringify is TRUE, teh species will be used to retreive the nodes and edges properties.
style	The default style when create the network
widths	The link width range.

Value

The network SUID.

Examples

data("ce.miRNA.map")
data("example.data")
data("ce.interactionmap")
data("ce.IDsMap")
sifNetwork<-buildNetwork(example.data$ce.bind, ce.interactionmap, level=2)
cifNetwork<-filterNetwork(rootgene=ce.IDsMap["DAF-16"], sifNetwork=sifNetwork, 
  exprsData=uniqueExprsData(example.data$ce.exprData, "Max", condenseName='logFC'),
  mergeBy="symbols",
  miRNAlist=as.character(ce.miRNA.map[ , 1]), tolerance=1)
gR<-polishNetwork(cifNetwork)
if(interactive()){
  cy3Network(gR)
}

jianhong/GeneNetworkBuilder documentation built on Nov. 4, 2024, 5:54 a.m.