outputgephi: use the phylsoeq object and cor matrix building Gephi input...
In taowenmicro/ggClusterNet:

outputgephi

R Documentation

use the phylsoeq object and cor matrix building Gephi input network file contain edge and node

Description

use the phylsoeq object and cor matrix building Gephi input network file contain edge and node

Usage

outputgephi(ps = ps, cor = cor)

Arguments

`ps`	phyloseq abject
`cor`	Correlation matrix

Value

result2 Which contains 2 lists.Result2[[1]], consists of OTU and its corresponding coordinates. Result2[[2]], consists of the network center coordinates of each group

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)
result = corMicro (ps = ps,N = 0.02,r.threshold=0.8,p.threshold=0.05,method = "pearson")
#Extract correlation matrix
cor = result[[1]]
gephi <- outputgephi(ps = result[[3]],cor =  cor)
edge_Gephi <- gephi[[1]]
head(edge_Gephi)
node_Gephi <- gephi[[2]]
head(node_Gephi)

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