GeneNetworkBuilder (version 1.14.3)

polishNetwork: generate an object of grahpNEL to represent the regulation network

Description

generate an object of grahpNEL to represent the regulation network. Each node will has three attributes: size, borderColor and fill.

Usage

polishNetwork(cifNetwork, 
				nodesDefaultSize=48, useLogFCAsWeight=FALSE, 
				nodecolor=colorRampPalette(c("green", "yellow", "red"))(5), nodeBg="white",
				nodeBorderColor=list(gene='darkgreen',miRNA='darkblue'), 
				edgelwd=0.25, ...)

Arguments

cifNetwork

dataframe used to draw network graph. column names of cifNetwork must contain 'from', 'to', 'logFC' and 'miRNA'

nodesDefaultSize

nodes default size

useLogFCAsWeight

how to determine the weights for each nodes. If TURE, use logFC value as weight. If FALSE, use constant 1 as weight.

nodecolor

a character vector of color set. The node color will be mapped to color set by log fold change

nodeBg

background of node

nodeBorderColor

a list of broder node color set. nodeBorderColor's element must be gene and miRNA

edgelwd

the width of edge

...

any parameters can be passed to graph.par

Value

An object of graphNEL class of the network

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)
##	g1<-Rgraphviz::layoutGraph(gR)
##	renderGraph(g1)
##	cat(saveXML(toGXL(g1)),sep="\n")