model_igraph: 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_igraph(cor = cor, method = "cluster_fast_greedy", seed = 12, Top_M = 20)

Arguments

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

Details

# The algorithm igraph 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

data.frame

Author(s)

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

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

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