corBionetwork: Microbial related bipartite network analysis

In taowenmicro/ggClusterNet:

Microbial related bipartite network analysis

Description

Microbial related bipartite network analysis

Usage

corBionetwork(
  otu = NULL,
  tax = NULL,
  map = NULL,
  ps = NULL,
  lab = NULL,
  N = 0,
  r.threshold = 0.6,
  p.threshold = 0.05,
  label = FALSE,
  group = "Group",
  env = NULL,
  envGroup = NULL,
  method = "spearman",
  layout = "fruchtermanreingold",
  path = "./",
  fill = "Phylum",
  size = "igraph.degree",
  scale = TRUE,
  bio = TRUE,
  zipi = FALSE,
  step = 100,
  width = 20,
  height = 20,
  big = TRUE,
  select_layout = TRUE,
  layout_net = "model_maptree",
  clu_method = "cluster_fast_greedy",
  minsize = 4,
  maxsize = 14
)

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=0.001, extract the top 0.001 relative abundance of OTU.
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.
label	Whether to add node label.
group	Separate Group.
env	Environmental factor index table which do network analysis with the microbiome.
envGroup	group of env table.
method	method for Correlation calculation,method="pearson" is the default value. The alternatives to be passed to cor are "spearman" and "kendall".
path	save path of all of network analyse.
fill	fill coulor of node.
size	node size.
scale	Whether relative abundance standardization is required.
bio	Do you need to do a binary network.
zipi	zipi Calculation.
step	Random network sampling times.
width	Save the width of the picture settings.
height	Save the height of the picture setting.
lay	layout which network show.

Value

list which contains OTU correlation matrix

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

path = "./netowrk/"
data(ps)
ps16s = ps %>% ggClusterNet::scale_micro()
psITS = NULL
library(phyloseq)
ps.merge <- ggClusterNet::merge16S_ITS(ps16s = ps16s,
                                       psITS = NULL,
                                       N16s = 100)
map =  phyloseq::sample_data(ps.merge)
head(map)
map$Group = "one"
phyloseq::sample_data(ps.merge) <- map
data(env1)
data1 = env1
data1$id = row.names(data1)
data1 = data1 %>% select(id,everything())
envRDA.s = vegan::decostand(env1,"hellinger")
data1[,-1] = envRDA.s
Gru = data.frame(ID = colnames(data1)[-1],group = "env" )
head(Gru)
corBionetwork(ps = ps.merge,
                            N = 0,
                            r.threshold = 0.4, # 相关阈值
                            p.threshold = 0.05,
                            big = T,
                            group = "Group",
                            env = data1, # 环境指标表格
                            envGroup = Gru,# 环境因子分组文件表格
                            # layout = "fruchtermanreingold",
                            path = path,# 结果文件存储路径
                            fill = "Phylum", # 出图点填充颜色用什么值
                            size = "igraph.degree", # 出图点大小用什么数据
                            scale = TRUE, # 是否要进行相对丰度标准化
                            bio = TRUE, # 是否做二分网络
                            zipi = F, # 是否计算ZIPI
                            step = 100, # 随机网络抽样的次数
                            width = 18,
                            label = TRUE,
                            height = 10
)

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