addMultiGraphToCytoscape: Add MultiNetworks 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 MultiNetworks into a Cytoscape session. This function automatically adds network styles for each class.

Usage

addMultiGraphToCytoscape(MultiNets, points.size.map = "PValue", min.points.value = 0.05,
	max.points.value = 0, points.fill.map = "FC", min.points.fill = -2,
	max.points.fill = 2, LayoutName = "force-directed", port.number = 1234)

Arguments

MultiNets	An object of class MultiNetworks
points.size.map	Node attribute for which the node size mapping is done. By default it is "PValue", which is the p-value from DE genes analysis results.
min.points.value	Maximum value of node attribute for which the size is minimal. By default it is 0.05.
max.points.value	Minimum value of node attribute for which the size is maximal. By default it is 0.
points.fill.map	Node attribute for which the node color mapping is done. By default it is the fold change.
min.points.fill	Minimum value for which the color mapping is done. By default it is -2.
max.points.fill	Maximum value for which the color mapping is done. By default it is 2.
LayoutName	The layout name used to display the network in Cytoscape. By default it is "force-directed".
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. This function adds network for each item in the network list, and a collection is attributed for each network class and factor level if used. This also adds automatically pre-defined styles for each network class.

See Also

addNetworkStyle, addGraphToCytoscape, MultiNetworks.default, 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,])

# MultiSpAData<-MultiDEGeneExpr(GaussianSpAData,DEGeneExpr(t(SpADataExpression[18:34,]),
#	SpADEGenes[18:34,]),DEGeneExpr(t(SpADataExpression[35:51,]),SpADEGenes[35:51,]))
# MultiSpANetworks<-MultiNetworks(MultiSpAData,
#	SelectInteractionsSTRING=c("coexpression","experimental","knowledge"),STRINGThreshold=0.9,
#	FilterSIMoNeOptions=list(Threshold=0.4),Factors=StatusFactor,
#	STRINGOptions=list(AddAnnotations=F),SIMoNeOptions=list(AddAnnotations=F),
#	WGCNAOptions=list(AddAnnotations=F))

# resetCytoscapeSession()
# addMultiGraphToCytoscape(MultiSpANetworks,points.size.map="P.Value",points.fill.map="logFC")

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