modulGroup: Correlation matrix calculates groups according to the degree...
In taowenmicro/ggClusterNet:

modulGroup

R Documentation

Correlation matrix calculates groups according to the degree of network module speech.

Description

Enter correlation matrix, calculate network modules, and generate groups.

Usage

modulGroup(corr = cor, cut = NULL, method = "cluster_walktrap")

Arguments

`cut`	which model contain node less than cut,will be tegether to other group,if NULL was assignment, will not to do with nothing.
`method`	method to culculate Degree of modularity.There are four module clustering algorithms inside.
`cor`	Correlation matrix

Details

# This is the function named 'modulGroup'# which Enter the correlation matrix. There are four module clustering algorithms inside, which can calculate the modularity and then group according to the modularity.

By default, returns table, contain node and group imformation The available method to culculate Degree of modularity include the following:

cluster_fast_greedy:
cluster_walktrap:
cluster_edge_betweenness:
cluster_spinglass:

Value

data table.

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 = 100,r.threshold=0.8,p.threshold=0.05,method = "pearson")
#Extract correlation matrix
cor = result[[1]]
# building the node group
netClu  = modulGroup( cor = cor,cut = 3,method = "cluster_fast_greedy" )
netClu$group = as.factor(netClu$group)
result2 = ranSNEClusterG (cor=  cor,layout ="circle")
node = result2[[1]]

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