edgeBuild: Construct edge files, add weights, positive and negative...
In taowenmicro/ggClusterNet:

edgeBuild

R Documentation

Construct edge files, add weights, positive and negative correlation and other basic information

Description

Construct edge files, add weights, positive and negative correlation and other basic information

Usage

edgeBuild(cor = cor, node = node)

Arguments

`cor`	Correlation matrix
`node`	Node file, containing calculated node coordinates

Value

edge which contains OTU and its coordinates, the correlation of edge between nodes

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 = 120,r.threshold=0.8,p.threshold=0.05,method = "pearson")
#Extract correlation matrix
cor = result[[1]]
# building the node group
netClu = data.frame(ID = row.names(cor),group =rep(1:3,length(row.names(cor)))[1:length(row.names(cor))] )
netClu$group = as.factor(netClu$group)
#Calculate node location
result2 = PolygonRrClusterG(cor = cor,nodeGroup = netClu )
node = result2[[1]]
edge = edgeBuild(cor = cor,node = node)

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