model_Gephi.2: This is the upgraded version.model_Gephi.2:The algorithm...

In taowenmicro/ggClusterNet:

This is the upgraded version.model_Gephi.2:The algorithm imitate Gephi's network layout. while, it saves time and the calculation speed is faster

Description

Enter correlation matrix, calculate network modules, and Calculate the coordinates of the node.

Usage

model_Gephi.2(cor = cor, method = "cluster_fast_greedy", seed = 2)

Arguments

cor	Correlation matrix Clustering Algorithm
method	Clustering Algorithm
seed	Set random seed

Details

# The algorithm imitate Gephi's network layout. while, it saves time and the calculation speed is faster,This is the upgraded version.

By default, returns a list

• cluster_fast_greedy:

• cluster_walktrap:

• cluster_edge_betweenness:

• cluster_spinglass:

Value

list

Author(s)

Contact: Tao Wen [e-mail] Penghao Xie [e-mail] yongxin liu [e-mail] Jun Yuan [e-mail]

References

Tao Wen#, Penghao Xie#, Shengdie Yang, Guoqing Niu, Xiaoyu Liu, Zhexu Ding, Chao Xue, Yong-Xin Liu *, Qirong Shen, Jun Yuan* ggClusterNet: an R package for microbiome network analysis and modularity-based multiple network layouts iMeta 2022,DOI: doi: 10.1002/imt2.32

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
result2 <- model_Gephi.2(cor = cor,
method = "cluster_fast_greedy",
seed = 12
)
node = result2[[1]]
node = result2[[2]]

taowenmicro/ggClusterNet documentation built on March 29, 2025, 1:04 p.m.