R packages：phyloseq（三） 16s 扩增子β多

导入数据

library("phyloseq")
library("ggplot2")
library(ggrepel)
library(ggsci)
library(MicrobiotaProcess)
otu <- "1_table-dada2_pe.qza"
rep <- "2_rep-seqs-dada2_pe.qza"
tree <- "3_rooted-tree_pe.qza"
tax <- "4_taxonomy_pe.qza"
sample <- "5_metadata.txt"
qiimedata <- import_qiime2(otuqza=otu, taxaqza=tax,refseqqza=rep,
                           mapfilename=sample,treeqza=tree)
qiimedata@sam_data[["group"]]<-factor(qiimedata@sam_data[["group"]],levels = c("Pre","Post"))

PCoA

生成排序矩阵

ordu<-ordinate(qiimedata,distance = 'uunifrac',
               method = "PCoA")

碎石图来查看排名前几的轴的贡献率

plot_scree(ordu)+ theme_bw()

碎石图.png

p1 <- plot_ordination(norm_qiimedata, ordu, color="group",shape = "group")
p1
p2<-p1+ 
  stat_ellipse()+ 
  theme_bw()+
  scale_color_aaas()+
  scale_fill_aaas(alpha=0.7)+
  geom_point(size = 5)
p2

PCoA.png

NMDS 非度量多维尺度分析

ordu = ordinate(qiimedata, "NMDS", "unifrac")
p1 <- plot_ordination(qiimedata, ordu, color="group",shape = "group")
p1
p2<-p1+ geom_line() + geom_point(size=5)+
  theme_bw()+scale_color_aaas()
p2

MDNS.png