Alpha多样性

• 多样性指数统计
• 多样性指数差异分析
• 稀释曲线
• Rank-Aundance曲线
• 物种累积曲线

https://gitee.com/bioinfoFungi/amplicon

使用USEARCH计算14种alpha多样性指数

http://www.drive5.com/usearch/manual/alpha_metrics.html

usearch -alpha_div results/otutab_rare.txt \
      -output results/alpha/alpha.txt

使用vegan包计算alpha多样性指数

otutab

library(vegan)
suppressMessages(library(tidyverse))
species = read.table("https://gitee.com/bioinfoFungi/amplicon/raw/master/results/otutab.txt", header=T, sep="\t", quote = "", row.names=1, comment.char="")
set.seed(1)
# min(colSums(species)) 抽样数使用最小值，或指定抽样数
depth <- 10000 
# vegan::rrarefy抽平至最小值或指定值
otu = vegan::rrarefy(t(species), depth) 
# 筛选大于抽样数量的样本
idx = rowSums(otu) >= depth
# 丢弃的样本列表
# rownames(otu[!idx,])
# 筛选大于抽样数量的样本的特征表
otu = otu[idx,]
## Alpha diversity
# vegan::estimateR计算obs, chao1和ACE指数
estimateR = t(estimateR(otu))[,c(1,2,4)]
colnames(estimateR) = c("richness", "chao1", "ACE")
# vegan::diversity计算多样性指数shannon, simpson和invsimpson
shannon = diversity(otu, index = "shannon")
simpson = diversity(otu, index = "simpson")
invsimpson = diversity(otu, index = "invsimpson")
# 合并6种指数
alpha_div = cbind(estimateR, shannon, simpson, invsimpson)
alpha_div

vegan