browseNetwork: browse network

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

browse network

Description

plot network generated by polishNetwork

Usage

browseNetwork(
  gR = graphNEL(),
  layoutType = c("fdp", "dot", "neato", "twopi", "circo"),
  width = NULL,
  height = NULL,
  maxNodes = 500,
  ...
)

Arguments

gR	an object of graphNEL
layoutType	layout type. see GraphvizLayouts
width	width of the figure
height	height of the figure
maxNodes	max nodes number to plot. Because if there are two many nodes, the running time will be too long.
...	parameters used by GraphvizLayouts

Value

An object of class htmlwidget that will intelligently print itself into HTML in a variety of contexts including the R console, within R Markdown documents, and within Shiny output bindings.

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 Oct. 26, 2023, 3:45 a.m.