ggvegan (version 0.2.1)

autoplot.isomap: ggplot-based plot for objects of class "isomap"

Description

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

Usage

# S3 method for 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,
  ...
)

Value

A ggplot object.

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.

Author

Gavin L. Simpson

Examples

library("vegan")

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

autoplot(ord)

autoplot(ord, geom = "text")