addFactorGraphsToCytoscape: Add FactorNetworks object to Cytoscape

In stringgaussnet: PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor

Description

This function allows to import an object of class FactorNetworks into a Cytoscape session.

Usage

addFactorGraphsToCytoscape(FactorNets, Name=deparse(substitute(FactorNets)),
	LayoutNames=rep("force-directed",length(FactorNets)),
	StyleNames=sapply(FactorNets,function(x) class(x[["Network"]])), port.number=1234)

Arguments

FactorNets	An object of class FactorNetworks
Name	The name of the added network in each collection
LayoutNames	The layout name to display the network in Cytoscape. By default it is "force-directed".
StyleNames	The style name to display the network in Cytoscape. We advice you to use addNetworkStyle() before this function. By default it is the network object class.
port.number	The local port number used by cyREST plugin to communicate with Cytoscape. By default it uses 1234.

Details

This function creates a collection for each level of factor, and adds the corresponding network in this collection. Cytoscape must be running during the use of this function.

See Also

checkCytoscapeRunning, addNetworkStyle, FactorNetworks.default

Examples

# data(SpADataExpression)
# data(SpADEGenes)
# data(SpASamples)
# SpAData<-DEGeneExpr(t(SpADataExpression),SpADEGenes)

# StatusFactor<-paste(SpASamples$status,SpASamples$b27,sep=".")
# names(StatusFactor)=SpASamples$chipnum

# NodesForSIMoNe<-rownames(SpADEGenes)[1:17]
# GaussianSpAData<-DEGeneExpr(t(SpADataExpression[NodesForSIMoNe,]),SpADEGenes[NodesForSIMoNe,])

# GlobalSIMoNeNetNF<-getSIMoNeNet(GaussianSpAData)
# GlobalSIMoNeNet<-FilterEdges(GlobalSIMoNeNetNF,0.4)

# StatusFactorSIMoNeNet<-FactorNetworks(GaussianSpAData,StatusFactor,"SIMoNe")
# StatusFactorSIMoNeNet<-FilterEdges(StatusFactorSIMoNeNet,0.4)

# resetCytoscapeSession()
# addNetworkStyle("SIMoNeNet",class(GlobalSIMoNeNet),points.size.map="P.Value",
#	points.fill.map="logFC")
# addFactorGraphsToCytoscape(StatusFactorSIMoNeNet)

stringgaussnet documentation built on May 29, 2017, 10:50 a.m.