Description Usage Arguments Details See Also Examples
View source: R/compareGaussNetworks.R
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.
1 2 3 | compareGaussNetworks(Network1, Network2, Names = c("Network1", "Network2"),
Colors = c("yellow", "blue", "green"), interactiveMode = T, RhoThreshold = 0.4,
PValueThreshold = 0.05)
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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 |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # 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"))
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