r语言做绘制精美pcoa图_R语言：Bary-Curtis PCoA

导读

Bary-Curtis PCoA降维分析菌群结构。

一、输入数据

1.1 菌属丰度矩阵

df = data.frame(abs(round(matrix(rnorm(729, 100, 50), 27, 27))))

rownames(df) = paste(rep(paste(rep(c("A", "B", "C"), each=3), rep(c("I","II","III")), sep=""), each=3), 1:3, sep="")

colnames(df) = paste("genus", 1:27, sep="")

1.2 样品分组

df_group = paste(rep(c("A", "B", "C"), each=9), rep(c("I","II","III"), each=3), sep="")

data.frame(rownames(df), df_group)

二、BC PCoA函数

library(vegan)

library(ggplot2)

library(ape)

pcoa_f = function(input, group)

{

pcoa = pcoa(vegdist(input, method