ggplot-based plot for envfit objects — autoplot.envfit • ggvegan

Produces a multi-layer ggplot object representing the output of objects produced by vegan::envfit().

Usage

# S3 method for class 'envfit'
autoplot(
  object,
  geom = c("label", "text", "label_repel", "text_repel"),
  line.col = "black",
  xlab = NULL,
  ylab = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ...
)

Arguments

object: an object of class "envfit", the result of a call to vegan::envfit().
geom: character; which geom to use to label vectors and factor centroids.
line.col: colour with which to draw vectors.
xlab: character; label for the x-axis.
ylab: character; label for the y-axis.
title: character; subtitle for the plot.
subtitle: character; subtitle for the plot.
caption: character; caption for the plot.
...: additional arguments passed to ggplot2::fortify().

Value

A ggplot object.

Author

Gavin L. Simpson

Examples


library("vegan")
data(varespec, varechem)
ord1 <- metaMDS(varespec)
#> Square root transformation
#> Wisconsin double standardization
#> Run 0 stress 0.1843196 
#> Run 1 stress 0.2633021 
#> Run 2 stress 0.2085514 
#> Run 3 stress 0.1825658 
#> ... New best solution
#> ... Procrustes: rmse 0.04163008  max resid 0.151824 
#> Run 4 stress 0.1825658 
#> ... Procrustes: rmse 2.44659e-05  max resid 8.075038e-05 
#> ... Similar to previous best
#> Run 5 stress 0.1969805 
#> Run 6 stress 0.196245 
#> Run 7 stress 0.224895 
#> Run 8 stress 0.1967393 
#> Run 9 stress 0.2048307 
#> Run 10 stress 0.2032569 
#> Run 11 stress 0.2095882 
#> Run 12 stress 0.1955836 
#> Run 13 stress 0.1825658 
#> ... New best solution
#> ... Procrustes: rmse 5.865506e-06  max resid 1.5389e-05 
#> ... Similar to previous best
#> Run 14 stress 0.18584 
#> Run 15 stress 0.2141074 
#> Run 16 stress 0.2032569 
#> Run 17 stress 0.2085949 
#> Run 18 stress 0.18458 
#> Run 19 stress 0.195049 
#> Run 20 stress 0.18458 
#> *** Best solution repeated 1 times
fit1 <- envfit(ord1, varechem, perm = 199)

autoplot(fit1, geom = 'label_repel')


data(dune, dune.env)
ord2 <- cca(dune)
fit2 <- envfit(ord2 ~ Moisture + A1, dune.env, perm = 199)

autoplot(fit2)