follow-up: Plotting ordiellipse function from vegan package onto NMDS plot created in ggplot2

问题

I am trying to do something similar to an old post: plotting - original post

For my analysis, I am interested in whether different mammal hosts have different flea communities. The original post I have linked to has 2 different solutions for the ellipses. My problem is when I run both the 1st solution and then the general solution I get vastly different looking plots while I think they should be very similar. Below is my code.

My question is: Am I doing something incorrectly or which code produces the correct figure? Or is there a better new code I should be using instead to display differences in flea communities by host species?

Thanks, Amanda

Link to ARG_comm data Link to ARG_env data

library(vegan)
library(BiodiversityR)
library(MASS)

comm_mat <- read.csv("d:/fleaID/ARG_comm.csv",header=TRUE)
env <- read.csv("d:/fleaID/ARG_env.csv",header=TRUE)

library(ggplot2)
sol <-metaMDS(comm_mat)
MyMeta=env

#originalresponse
NMDS = data.frame(MDS1 = sol$points[,1],     MDS2=sol$points[,2],group=MyMeta$host)
NMDS.mean=aggregate(NMDS[,1:2],list(group=NMDS$group),mean)

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))
}

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)

#update - can use se (standard error) or sd (standard dev)
#update
NMDS = data.frame(MDS1 = sol$points[,1], MDS2 =        sol$points[,2],group=MyMeta$host)

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

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))
}

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)

回答1:

There are two key differences between the first and second plot methods. The first method is calculating the ellipse paths using standard deviation and no scaling. The second method is using standard error and is also scaling the data. Thus, the plot produced with the first method can also be achieved with the second method by making the necessary changes to the ordiellipse function (kind='sd', not 'se'), and removing the scale (ord[[g]]$scale) from the veganCovEllipse function. I have included this below so you can see for yourself.

Ultimately, both plots are correct, it just depends on what you want to show. As long as you specify the use of standard error or deviation, either can be used. As for whether or not to scale, this really depends on your data. This link may be helpful: Understanding `scale` in R.

First method:

sol <-metaMDS(comm_mat)
MyMeta=env

#originalresponse
NMDS = data.frame(MDS1 = sol$points[,1],     MDS2=sol$points[,2],group=MyMeta$host)
NMDS.mean=aggregate(NMDS[,1:2],list(group=NMDS$group),mean)

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))
}

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)

Gives:

Second method:

plot.new()

ord<-ordiellipse(sol, MyMeta$host, display = "sites", 
                 kind = "sd", conf = .95, label = T)

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)))
            ,group=g))
}

plot2<-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)+
  annotate("text",x=NMDS.mean$MDS1,y=NMDS.mean$MDS2,label=NMDS.mean$group)

plot2

Also gives:

来源：https://stackoverflow.com/questions/42799838/follow-up-plotting-ordiellipse-function-from-vegan-package-onto-nmds-plot-creat

标签

ggplot2

vegan