1、NMDS非度量多维尺度分析作图（R）

导入VOTU.txt , 每列为不同的样本，每行为不同的vOTU

导入分组文件，此处有两种分组方式。后续分别按颜色和形状分类

library(ggplot2)
library(vegan)
# 读取NMDS数据文件
df = read.delim("C:/Users/Shizhe Zhang/Desktop/VOTU.txt",
                header = T,    # 指定第一行是列名
                row.names = 1  # 指定第一列是行名
)
df=t(df) # 对数据进行转置。
# 读取样本分组数据文件
dfGroup = read.delim("C:/Users/Shizhe Zhang/Desktop/分组信息.txt",row.names = 1)
# NMDS计算
dfNmds<-metaMDS(df,distance="bray",k = 2)
# 绘图前的数据整理
data = data.frame(dfNmds$points)   #绘点
data$group = dfGroup$region        #分组1
data$group2 = dfGroup$species      #分组2
# 绘图
ggplot(data,aes(x = MDS1,
                y = MDS2,
                color = group,
                group = group,
                shape = group2,
                fill = group)
)+
  geom_point(size=2)+
  scale_shape_manual(values=c(0,5,2,1,6,16,15))+     #设置形状
  scale_fill_manual(values=c("#FF00FF","#FFFF00","#D9D500","#0000FF","#00FFFF","#007DFF","#FF00AA","#B5B200","#FF0055","#FF0000"))+            #设置颜色
  scale_color_manual(values=c("#FF00FF","#FFFF00","#D9D500","#0000FF","#00FFFF","#007DFF","#FF00AA","#B5B200","#FF0055","#FF0000"))+
  theme_classic()+
  labs(                     # 在副标题处添加stress
    subtitle = paste("stress=",round(dfNmds$stress,5),sep="")
  )