ggplot-based plot for objects of class "isomap"

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

Usage

# S3 method for class 'isomap'
autoplot(
  object,
  axes = c(1, 2),
  geom = c("point", "text"),
  network = TRUE,
  line.col = "grey85",
  linewidth = 0.7,
  xlab = NULL,
  ylab = NULL,
  title = "Isometric feature mapping",
  subtitle = NULL,
  caption = NULL,
  ...
)

Arguments

object: an object of class "isomap", the result of a call to vegan::isomap().
axes: numeric; which axes to plot, given as a vector of length 2.
geom: character; which geom to use for the MDS scores layer.
network: logical; should the edges of the ISOMAP network be drawn?
line.col: colour with which to draw the network edges.
linewidth: numeric; linewidth aesthetic for the log-series curve.
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 other methods.

Value

A ggplot object.

Author

Gavin L. Simpson

Examples


library("vegan")

data(BCI)
dis <- vegdist(BCI)
ord <- isomap(dis, k = 3)

autoplot(ord)


autoplot(ord, geom = "text")