saveCytoscapeSession: Save Cytoscape session

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

Description

This function allows to save all networks and styles from a Cytoscape session in a file.

Usage

saveCytoscapeSession(filepath = "stringgaussnet_networks", overwrite = F, absolute = F,
	port.number = 1234)

Arguments

filepath	Where will be saved the Cytoscape session
overwrite	A boolean variable indicating whether the file must be overwritten
absolute	A boolean variable indicating whether filepath is an absolute path. If not, the R work directory is added before filepath.
port.number	The local port number used by cyREST plugin to communicate with Cytoscape. By default it uses 1234.

Details

The file extension .cys is automatically added in the file path. The variable absolute is important because the work directories for cyREST and R are not the same.

See Also

addGraphToCytoscape

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)

# resetCytoscapeSession()
# addNetworkStyle("SIMoNeNet",class(GlobalSIMoNeNet),points.size.map="P.Value",
#	points.fill.map="logFC")
# NetId<-addGraphToCytoscape(GlobalSIMoNeNet)
# saveCytoscapeSession("SIMoNeNet")

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