ggraph包优雅的绘制网络图

本节来介绍如何基于微生物测序得到的OTU表绘制一个物种间网络图，下面通过一个小栗子来进行展示

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加载并安装R包

package.list=c("tidyverse","ggraph","tidygraph","magrittr","tidytext","widyr")

for (package in package.list) {
  if (!require(package,character.only=T, quietly=T)) {
    install.packages(package)
    library(package, character.only=T)
  }
}

导入数据

otu <- read_tsv("otu_taxa_table.xls") %>% 
  separate(taxonomy,
           into=c("domain","phylum","class","order","family","genus","species"),sep=";") %>% 
  mutate_at(vars(c(`domain`:`species`)),~str_split(.,"__",simplify=TRUE)[,2]) %>% 
  column_to_rownames("OTU")

数据拆分

table <- otu %>% select_if(~is.numeric(.)) %>% rownames_to_column("ID")
tax