8  Network analysis

Networks can represent various systems in the real world,and have many applications in biological research,especially in systems biology: gene expression regulatory networks,metabolic networks,ecosystem space networks,microbial co-occurrence networks,protein interaction networks,etc.

MetaNet is a comprehensive network analysis package, especially in various biological omics.

The latest development version can be found in https://github.com/Asa12138/MetaNet.

Please go to https://asa12138.github.io/MetaNet_tutorial/ for the full vignette.

library(MetaNet)

t(otutab) -> totu
c_net_cal(totu) -> corr
c_net_build(corr, r_thres = 0.65) -> co_net

c_net_plot(co_net)

Figure 8.1: Simple correlation network

co_net <- c_net_set(co_net, taxonomy, data.frame("Abundance" = colSums(totu)),
  vertex_class = "Phylum", vertex_size = "Abundance"
)
c_net_plot(co_net)

Figure 8.2: Simple correlation network with annotation