3

我正在尝试通过以下函数在数据集上通过 vegan 包应用 NMDS：

library(vegan)
library(MASS)
library(MVA)
library(ggplot2)
all_d <- vegdist(landmetr, method= "hor", binary=FALSE, diag=TRUE,
             upper=FALSE, na.rm = FALSE)
allmds3 <- isoMDS(all_d, k=3)
gr0 <- factor(france100_7c$LAND_CODE)
plot(allmds3$points[,2:3], col=gr0, bg="grey", cex=0.2,pch=20) 
# regress environmental variables on configuration of site points
provaenv3 <- envfit(allmds3$points[,2:3], landmetr,999, na.rm = FALSE, france100_7c$LAND_CODE)
# add the environmental regressions to the area plot
plot(provaenv3,add=T, cex=0.5)
#plot0
ordiellipse (allmds3, gr0, kind = "sd", conf=0.95, label = T)

然而，尽管这个双标图是在轴 2 和 3 上构建的，但 ordiellipse 函数会编写用于标识轴 1 和 2 双标图上的集群的椭圆。谁能解释我为什么会发生这种情况以及我如何在轴 2 和 3 双图上绘制正确的椭圆？

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2 回答 2

2

在这种情况下，预期的用途也是传递choices给ordiellipse。如中所述?ordiellipse

 ...: Parameters passed to graphical functions or to ‘scores’ to
      select axes and scaling etc.

因此@EDi 的例子可以更简单地完成

library("vegan")
data(dune)
data(dune.env)
set.seed(1234)
NMDS <- metaMDS(dune, k = 3)
take <- c(1,3)
plot(NMDS, choices = take, display = "sites", type = "n")
points(NMDS, choices = take, display = "sites",
       col = dune.env$Management)
with(dune.env, ordiellipse(NMDS, Management, choices = take))

生产

在此处输入图像描述

于 2015-07-15T14:13:22.947 回答
1

您可以使用替代绘图功能ordiplot()：

require(vegan)
data(dune)
data(dune.env)
NMDS <- metaMDS(dune, k = 3)
pl<-ordiplot(NMDS, choices = c(2, 3), display = 'sites', type = 'n')
points(pl, what = 'sites', col = dune.env$Management, pch = 16)
ordiellipse(pl, dune.env$Management)
于 2015-07-15T11:06:26.130 回答