network.2: Microbial related network
In taowenmicro/ggClusterNet:

network.2

R Documentation

Microbial related network

Description

Microbial related network

Usage

network.2(
  otu = NULL,
  tax = NULL,
  map = NULL,
  ps = NULL,
  N = 0,
  big = FALSE,
  select_layout = FALSE,
  layout_net = "model_maptree2",
  r.threshold = 0.6,
  p.threshold = 0.05,
  maxnode = 2,
  method = "spearman",
  label = FALSE,
  lab = "elements",
  group = "Group",
  path = "./",
  fill = "Phylum",
  size = "igraph.degree",
  scale = TRUE,
  zipi = FALSE,
  clu_method = "cluster_fast_greedy",
  step = 100,
  yourmem = theme_void(),
  ncol = 3,
  nrow = 1,
  R = 10,
  ncpus = 1
)

Arguments

`ps`	phyloseq Object, contains OTU tables, tax table and map table, represented sequences,phylogenetic tree.
`N`	filter OTU tables by abundance.The defult, N=0, extract the top N number relative abundance of OTU. e.g 100
`big`	TRUE or FALSE the number of micro data was so many (> 300),you can chose TREU
`select_layout`	TURE or FALSE
`layout_net`	select layout from ggClusterNet
`r.threshold`	The defult, r.threshold=0.6, it represents the correlation that the absolute value of the correlation threshold is greater than 0.6. the value range of correlation threshold from 0 to 1.
`p.threshold`	The defult, p.threshold=0.05, it represents significance threshold below 0.05.
`method`	method for Correlation calculation,method="pearson" is the default value. The alternatives to be passed to cor are "spearman" and "kendall".
`label`	Whether to add node label.
`group`	Separate Group.
`path`	save path of all of network analyse.
`fill`	fill coulor of node
`size`	node size
`zipi`	zipi Calculation
`step`	Random network sampling times
`R`	repeat number of p value calculate
`ncpus`	number of cpus used for sparcc
`lay`	layout which network show

Value

list which contains OTU correlation matrix

Author(s)

Contact: Tao Wen taowen@njau.edu.cn Penghao Xie 2019103106@njau.edu.cn yongxin liu yxliu@genetics.ac.cn Jun Yuan junyuan@njau.edu.cn

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)
path = "./netowrk/"
dir.create(path)
result = network.2(ps = ps,N = 100,r.threshold=0.6,big = T,
                   select_layout = T,
                   p.threshold=0.05,label = FALSE,path = path ,zipi = F)
result[[1]]
result[[2]]

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