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

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

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. The size will be mapped to the length of its edges. The node fill color will be mapped to logFC.

Usage

polishNetwork(
  cifNetwork,
  nodeData,
  nodesDefaultSize = 48,
  nodecolor = colorRampPalette(c("green", "yellow", "red"))(5),
  nodeBg = "white",
  nodeBorderColor = list(gene = "darkgreen", miRNA = "darkblue"),
  edgeWeight = NA,
  edgelwd = 0.5,
  ...
)

Arguments

cifNetwork	dataframe used to draw network graph. column names of cifNetwork must contain 'from', 'to', 'logFC' and 'miRNA'
nodeData	The node data. If it is not provide, node data will be retrieved from cifNetwork for the 'to' nodes.
nodesDefaultSize	nodes default size
nodecolor	a character vector of color set. The node color will be mapped to color set by log fold change. Or the column names for the colors.
nodeBg	background of node
nodeBorderColor	a list of broder node color set. nodeBorderColor's element must be gene and miRNA
edgeWeight	the weight of edge. It can be a column name of cifNetwork.
edgelwd	the default width of edge. If edgeWeight is set, the edgelwd will be mapped to the edgeWeight.
...	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)
##	browseNetwork(gR)

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