compareGaussNetworks: Compare gaussian networks

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

Description

A function to compare gaussian networks. It was originally created to compare between SIMoNe and WGCNA networks, but you can compare any network with nodes in common.

Usage

compareGaussNetworks(Network1, Network2, Names = c("Network1", "Network2"),
	Colors = c("yellow", "blue", "green"), interactiveMode = T, RhoThreshold = 0.4,
	PValueThreshold = 0.05)

Arguments

Network1	First gaussian network to compare
Network2	Second gaussian network to compare
Names	Names attributed to networks
Colors	Colors attributed to first, second and common networks
interactiveMode	Boolean variable indicating whether the plots are in interactive mode. If false, it is useful for automatically saving plots in a single pdf file.
RhoThreshold	Threshold to display vertical dashed line in the last plot
PValueThreshold	Threshold to display horizontal dashed line in the last plot

Details

Firstly, the function plots a venn diagram to compare network connectivities. Then we can see a series of boxplots displaying absolute values of rhos and spearman's p-values in the first network, the second network and the common network. Afterwards, we see mean node connectivities in each network, and finally a plot of spearman's p-values as a function of rhos.

See Also

compareFactorNetworks

Examples

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

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

# pickWGCNAParam(GaussianSpAData)
# GlobalWGCNANet<-getWGCNANet(GaussianSpAData)
# print(GlobalWGCNANet,5)
# summary(GlobalWGCNANet)
# plot(GlobalWGCNANet)
# export(GlobalWGCNANet,"GlobalWGCNANet",T)

# compareGaussNetworks(GlobalSIMoNeNet,GlobalWGCNANet,c("SIMoNe","WGCNA"))

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