ggplot-based plot for envfit objects

Produces a multi-layer ggplot object representing the output of objects produced by isomap.

# 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 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 fortify.

Value

A ggplot object.

Author

Gavin L. Simpson

Examples

data(varespec, varechem)
ord1 <- metaMDS(varespec)
#> Square root transformation
#> Wisconsin double standardization
#> Run 0 stress 0.1843196 
#> Run 1 stress 0.1955836 
#> Run 2 stress 0.1967393 
#> Run 3 stress 0.1967393 
#> Run 4 stress 0.1976151 
#> Run 5 stress 0.2426846 
#> Run 6 stress 0.2154149 
#> Run 7 stress 0.1948413 
#> Run 8 stress 0.2109006 
#> Run 9 stress 0.2175654 
#> Run 10 stress 0.2493007 
#> Run 11 stress 0.196245 
#> Run 12 stress 0.2370314 
#> Run 13 stress 0.2096851 
#> Run 14 stress 0.2301606 
#> Run 15 stress 0.2409076 
#> Run 16 stress 0.1974409 
#> Run 17 stress 0.1869637 
#> Run 18 stress 0.2360867 
#> Run 19 stress 0.18458 
#> ... Procrustes: rmse 0.04934599  max resid 0.1574658 
#> Run 20 stress 0.18458 
#> ... Procrustes: rmse 0.04935325  max resid 0.157505 
#> *** Best solution was not repeated -- monoMDS stopping criteria:
#>     18: stress ratio > sratmax
#>      2: scale factor of the gradient < sfgrmin
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)