从vegan包绘制ordiellipse函数到ggplot2中创建的NMDS图

Question

而不是我ggplot2用来创建NMDS图的正常绘图功能.我想在使用功能的NMDS阴谋显示组ordiellipse()从vegan包.

示例数据:

library(vegan)
library(ggplot2)
data(dune)
# calculate distance for NMDS
sol <- metaMDS(dune)
# Create meta data for grouping
MyMeta = data.frame(
  sites = c(2,13,4,16,6,1,8,5,17,15,10,11,9,18,3,20,14,19,12,7),
  amt = c("hi", "hi", "hi", "md", "lo", "hi", "hi", "lo", "md", "md", "lo", 
          "lo", "hi", "lo", "hi", "md", "md", "lo", "hi", "lo"),
  row.names = "sites")
# plot NMDS using basic plot function and color points by "amt" from MyMeta
plot(sol$points, col = MyMeta$amt)
# draw dispersion ellipses around data points
ordiellipse(sol, MyMeta$amt, display = "sites", kind = "sd", label = T)

# same in ggplot2
NMDS = data.frame(MDS1 = sol$points[,1], MDS2 = sol$points[,2])
ggplot(data = NMDS, aes(MDS1, MDS2)) + 
  geom_point(aes(data = MyMeta, color = MyMeta$amt))

如何将ordiellipse添加到使用ggplot2？创建的NMDS图中？

Didzis Elferts的回答非常有用.谢谢!但是,我现在有兴趣将以下ordiellipse绘制到创建的NMDS图ggplot2:

ordiellipse(sol, MyMeta$amt, display = "sites", kind = "se", conf = 0.95, label = T)

不幸的是,我不太了解该veganCovEllipse功能如何能够自己调整脚本.

Answer 1

首先,我将列组添加到您的NMDS数据框中.

  NMDS = data.frame(MDS1 = sol$points[,1], MDS2 = sol$points[,2],group=MyMeta$amt)

第二个数据框包含每个组的平均MDS1和MDS2值,它将用于在图上显示组名

  NMDS.mean=aggregate(NMDS[,1:2],list(group=group),mean)

数据框df_ell包含显示省略号的值.它是用veganCovEllipse隐藏在vegan包中的功能计算的.此功能应用于NMDS(组)的每个级别,并且还使用函数cov.wt来计算协方差矩阵.

  veganCovEllipse<-function (cov, center = c(0, 0), scale = 1, npoints = 100) 
  {
    theta <- (0:npoints) * 2 * pi/npoints
    Circle <- cbind(cos(theta), sin(theta))
    t(center + scale * t(Circle %*% chol(cov)))
  }

  df_ell <- data.frame()
  for(g in levels(NMDS$group)){
    df_ell <- rbind(df_ell, cbind(as.data.frame(with(NMDS[NMDS$group==g,],
                    veganCovEllipse(cov.wt(cbind(MDS1,MDS2),wt=rep(1/length(MDS1),length(MDS1)))$cov,center=c(mean(MDS1),mean(MDS2)))))
                    ,group=g))
  }

现在用函数绘制椭圆,geom_path()并annotate()用于绘制组名.

  ggplot(data = NMDS, aes(MDS1, MDS2)) + geom_point(aes(color = group)) +
    geom_path(data=df_ell, aes(x=MDS1, y=MDS2,colour=group), size=1, linetype=2)+
    annotate("text",x=NMDS.mean$MDS1,y=NMDS.mean$MDS2,label=NMDS.mean$group)

椭圆绘图的想法是从另一个stackoverflow 问题中采用的.

更新 - 在两种情况下都有效的解决方案

首先,使用组列制作NMDS数据框.

NMDS = data.frame(MDS1 = sol$points[,1], MDS2 = sol$points[,2],group=MyMeta$amt)

接下来,将函数的结果保存ordiellipse()为某个对象.

ord<-ordiellipse(sol, MyMeta$amt, display = "sites", 
                   kind = "se", conf = 0.95, label = T)

数据框df_ell包含显示省略号的值.它再次使用veganCovEllipse隐藏在vegan包中的功能进行计算.该函数被施加到NMDS(组)的每个电平,现在,它使用存储在参数ord对象- cov,center和scale每个级别的.

df_ell <- data.frame()
for(g in levels(NMDS$group)){
  df_ell <- rbind(df_ell, cbind(as.data.frame(with(NMDS[NMDS$group==g,],
                  veganCovEllipse(ord[[g]]$cov,ord[[g]]$center,ord[[g]]$scale)))
                                ,group=g))
}

绘图的方式与前面的例子相同.至于ordiellipse()使用elipses对象的坐标计算,此解决方案将使用您为此功能提供的不同参数.

ggplot(data = NMDS, aes(MDS1, MDS2)) + geom_point(aes(color = group)) +
  geom_path(data=df_ell, aes(x=NMDS1, y=NMDS2,colour=group), size=1, linetype=2)