stringgaussnet (version 1.0)

compareGaussNetworks: Compare gaussian networks

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"))