Alpha多样性

最后发布时间 : 2022-11-04 11:55:57 浏览量 :

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

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

Sample	berger_parker	buzas_gibson	chao1	dominance	equitability	jost	jost1	reads	richness	robbins	simpson	shannon_e	shannon_2	shannon_10
KO1	0.0584	0.0358	1211.1	0.99	0.828	172.6	357.9	10000	1210	0.258	0.0102	5.88	8.48	2.55
KO2	0.0536	0.0385	1198.8	0.992	0.84	202.5	385.2	10000	1198	0.239	0.00827	5.95	8.59	2.59
KO3	0.0658	0.0273	1052.3	0.988	0.806	140.1	273.2	10000	1051	0.298	0.0116	5.61	8.09	2.44
KO4	0.0598	0.0278	1051.2	0.989	0.809	145.9	278.4	10000	1050	0.275	0.0109	5.63	8.12	2.44
KO5	0.0727	0.0226	968.9	0.986	0.789	112.6	226.2	10000	968	0.282	0.0144	5.42	7.82	2.35
KO6	0.0503	0.0333	1119	0.991	0.827	179.1	332.6	10000	1118	0.256	0.00888	5.81	8.38	2.52

使用vegan包计算alpha多样性指数

#OTUID	KO1	KO2	KO3	KO4	KO5	KO6	OE1	OE2	OE3	OE4	OE5	OE6	WT1	WT2	WT3	WT4	WT5	WT6
ASV_1	382	671	282	438	381	390	476	590	500	360	490	357	799	830	567	664	508	519
ASV_2	671	412	863	793	1032	631	245	169	414	440	348	239	440	536	267	386	497	424
ASV_3	213	173	369	296	445	308	211	151	372	367	316	242	327	635	357	416	413	274
ASV_4	506	141	181	257	480	178	203	196	134	210	214	129	362	473	196	192	394	290
ASV_8	189	195	215	148	77	101	132	183	540	300	211	190	230	275	199	356	169	184
ASV_6	302	232	307	309	490	365	89	95	114	143	134	137	178	191	154	184	158	158

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

SampleID	richness	chao1	ACE	shannon	simpson	invsimpson
KO1	1210	1439.9336492891	1433.18771126219	5.88030042614566	0.98975464	97.6051597991676
KO2	1198	1376.43913043478	1399.75229527834	5.95381577180023	0.99172944	120.910796850516
KO3	1051	1298.8578680203	1318.90880535978	5.61028156370725	0.98841646	86.3293949863341
KO4	1050	1274.95135135135	1267.60312612405	5.62923484359834	0.98911074	91.8336048546917
KO5	968	1152.71641791045	1191.25655835447	5.42149950885837	0.98560856	69.4857498624182
KO6	1118	1315.3125	1328.64990957236	5.80703938504695	0.99112052	112.619207431066

vegan

等量抽样标准化 Beta多样性