div_network: Calculate a bipartite network for microbiome data
In taowenmicro/ggClusterNet:

div_network

R Documentation

Calculate a bipartite network for microbiome data

Description

Calculate a bipartite network for microbiome data

Usage

div_network(ps, group = "Group", flour = TRUE, N = 0.5)

Arguments

`ps`	phyloseq Object, contains OTU tables, tax table and map table, represented sequences,phylogenetic tree.
`flour`	Is the arrangement of points discrete? TRUE or FEASE would be selected
`num`	Number of samples per group.

Value

list

Author(s)

Contact: Tao Wen 2018203048@njau.edu.cn Jun Yuan junyuan@njau.edu.cn Penghao Xie 2019103106@njau.edu.cn

References

Yuan J, Zhao J, Wen T, Zhao M, Li R, Goossens P, Huang Q, Bai Y, Vivanco JM, Kowalchuk GA, Berendsen RL, Shen Q Root exudates drive the soil-borne legacy of aboveground pathogen infection Microbiome 2018,DOI: doi: 10.1186/s40168-018-0537-x

Examples

data(ps)
ps_sub = filter_taxa(ps, function(x) sum(x ) > 20 , TRUE)
ps_sub = filter_taxa(ps_sub, function(x) sum(x ) < 30 , TRUE)
ps_sub

result = div_network(ps_sub,num = 6)

edge = result[[1]]
head(edge)

taowenmicro/ggClusterNet documentation built on March 29, 2024, 1:32 a.m.