ranSNEClusterG: Use the layout in the sne package to calculate the visual...
In taowenmicro/ggClusterNet:

ranSNEClusterG

R Documentation

Use the layout in the sne package to calculate the visual layout of the network

Description

Use the layout in the sne package to calculate the visual layout of the network

Usage

ranSNEClusterG(cor = cor, layout = "circle", nodeGroup = netClu, zoom = 1)

Arguments

`cor`	Correlation matrix
`layout`	select layout to building sub cluster，could br on of the sna package layout, such as "circle","adj","circrand","eigen","random".
`nodeGroup`	group you must imput
`zoom`	Set the distance between modules

Value

list

Author(s)

Contact: Tao Wen 2018203048@njau.edu.cn Jun Yuan junyuan@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
data(ps)
result = corMicro (ps = ps,N = 100,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)
result2 = ranSNEClusterG (cor=  cor,layout ="circle",nodeGroup = netClu)
node = result2[[1]]

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