微生物共现网络模块的遗传发育特征分析

  对微生物OTU表进行网络分析有利于我们进一步挖掘微生物群落格局背后的构建因素。影响微生物共现网络的两个主要因素为：环境筛选和微生物交互作用，而这两者背后都有一个共同的影响因素——遗传发育特征。我们之前介绍了如何探究环境因子对微生物共现网络的影响，这里我们将分析微生物共现网络模块的遗传发育特征，以期回答这样一个问题：属于同一模块的OTUs是否具有更相似的遗传发育特征？

1. Load R package

library(igraph)
library(vegan)
library(picante)
library(ape)

2. Load test data

igraph <- read_graph("~/Desktop/htl_data_analysis/R code/netwok and env/mygraph.graphml",format="graphml")
tree <- read.tree("~/Desktop/htl_data_analysis/R code/netwok and env/tree")
nifh_otu2 <- read.delim("~/Desktop/htl_data_analysis/R code/netwok and env/nifh_otu.txt", row.names=1)

3. Modular division and get the top 4 cluster ID

wtc <- cluster_louvain(igraph,NA)
modularity(wtc)
V(igraph)$module<-membership(wtc)
modtop4 <- order(tabulate(membership(wtc)),decreasing=TRUE)[1:4] 

4. Build new OTU table for NTI analysis

rlen <- length(modtop4)+1
#clen <- sum(tabulate(membership(wtc))[modtop4])
clen <- ncol(nifh_otu2)
#otu_new <- matrix(rep(0,rlen*clen),rlen,clen,dimnames=list(modtop4,V(igraph)$name[V(igraph)$module%in%modtop4]))
otu_new <- matrix(rep(0,rlen*clen),rlen,clen,dimnames=list(c(modtop4,"other"),colnames(nifh_otu2)))
for (i in 1:rlen){
  if (i < rlen){
    otu_new[i,] = as.integer(colnames(otu_new) %in% V(igraph)$name[V(igraph)$module==modtop4[i]])
  }
  else{
    otu_new[i,] = as.integer(!(colnames(otu_new) %in% V(igraph)$name[V(igraph)$module %in% modtop4]))
  }
}
otu_new[1:5,1:5]

5. Tidy the tree and OTU table data for NTI analysis

tree$tip.label <- stringr::str_replace_all(tree$tip.label,"'","")

prune_tree<-prune.sample(nifh_otu2,tree)
tip<-prune_tree$tip.label
coln<-colnames(otu_new)
m<-NULL
print("These OTUs don't exist in phylogenetic tree")
for(i in 1:length(coln)){
  if(!coln[i]%in%tip){
    print(coln[i])
    m<-cbind(m,coln[i])
  }
}
m<-as.vector(m)
otu_new2<-otu_new[,!colnames(otu_new)%in%m]

6. Get the NTI result of each cluster

otu_phydist <- cophenetic(prune_tree)
mntd_wei<-ses.mntd(otu_new2, otu_phydist, null.model="taxa.labels", abundance.weighted=FALSE, runs=999)

[1] 运行效果可查看如下链接：
运行效果：https://rpubs.com/longroad/884091
[2] 测试数据及源代码可查看如下链接：
面包多：探究共现网络遗传发育特征测试数据及源代码
[2] 更多R语言分析微生物生态学的资源可参考如下链接：
https://mbd.pub/o/bread/mbd-YpmTlZpr