Add ordisurf Result as Contours to an Ordination Graph

Function adds vegan::ordisurf() results to an graph.

Usage

# S3 method for class 'ordisurf'
autolayer(
  object,
  fill = FALSE,
  contour.params = list(),
  fill.params = list(),
  ...
)

Arguments

object: vegan::ordisurf() result object.
fill: Use filled ordination space where raster colour match the fitted values of the surface (logical).
contour.params, fill.params: Arguments passed to ggplot2::geom_contour() or to ggplot2::geom_raster(), respectively.
...: Other arguments passed both to ggplot2::geom_contour() and ggplot2::geom_raster().

Value

Returns ggplot2 layers geom_contour and geom_raster (optionally).

Details

Function draws contours of fitted vegan::ordisurf() surface and (optionally) a raster of the surface using ggplot2::geom_contour() and ggplot2::geom_raster().

Function uses gridded values of ordination plane saved within the vegan::ordisurf() result instead of scores data from an ordination object. Therefore its results can be added to any ordination graph, also from autoplot methods. However, you must be careful with using exactly the same axes and scaling in vegan::ordisurf() object and ordination.

Surface fill is non-transparent and will paint over all previous layers. Filled surface should be used before other visible layers, or fill should be made transparent with alpha in argument fill.params passed to ggplot2::geom_raster().

Author

Jari Oksanen

Examples

library(vegan)
library(ggplot2)
data(mite, mite.env, package="vegan")
mod <- cca(mite)
surf <- ordisurf(mod ~ WatrCont, mite.env, plot = FALSE)
ordiggplot(mod) +
  geom_ordi_point("sites", size = mite.env$WatrCont/100) +
  autolayer(surf) +
  autolayer(envfit(mod ~ WatrCont, mite.env, permutations=0),
    arrow.mul = 1.3)