plot_network: plot_network

In gongcongcong/mbOmic: Integrative analysis of the microbiome and metabolome

plot_network

Description

plotting the network of metabolites and OTU. Orange nodes represent the OTU, while the other color represent the metabolite. Same color metabolites nodes are constructed in the same modules.

Usage

plot_network(net, corr, seed = 123, return = FALSE, interaction = TRUE)

Arguments

net	result of function 'coExpress'
corr	result of function 'corr.test'
seed	set seed for layout in interaction ploting
return	whether return the igraph
interaction	plot method

Value

igraph or graph

Author(s)

Congcong Gong

Examples

library(data.table)
path <- system.file('extdata', 'metabolites_and_genera.rda', package = 'mbOmic')
load(path)
names(genera)[1] <- 'rn'
names(metabolites)[1] <- 'rn'
b <- bSet(b = genera)
m <- mSet(m = metabolites)
res <- corr(m, b, method = 'spearman')
net <- coExpress(m, minN = 2, power = 9, message = FALSE)
plot_network(net, res[abs(rho)>=0.85])

gongcongcong/mbOmic documentation built on July 1, 2023, 1:47 p.m.