addGraphToCytoscape: Add network to Cytoscape

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

Description

This function allows to import a network created from the stringgaussnet package into Cytoscape, with the use of the cyREST plugin.

Usage

addGraphToCytoscape(Network, Collection = class(Network),
	Name = deparse(substitute(Network)), LayoutName = "force-directed",
	StyleName = Collection, port.number = 1234)

Arguments

Network	A network object from the stringgaussnet package. Can be of class STRINGNet, ShortPathSTRINGNet, SIMoNeNet or WGCNANet.
Collection	The collection name used in Cytoscape. By default it is the network object class.
Name	The network name used in Cytoscape
LayoutName	The layout name to display the network in Cytoscape. By default it is "force-directed".
StyleName	The style name to display the network in Cytoscape. We advice you to use addNetworkStyle() before this function. By default it is the collection name.
port.number	The local port number used by cyREST plugin to communicate with Cytoscape. By default it uses 1234.

Details

Cytoscape must be running during the use of this function, with the activation of the cyREST plugin. Please see checkCytoscapeRunning() for more details.

Value

The network ID in the Cytoscape session.

See Also

addNetworkStyle, checkCytoscapeRunning

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)

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