vegan3d: orditree3d – R documentation

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orditree3d

Draw Cluster Tree over a Plane

Description

Function draws a 3D plot where ordination result is at the bottom plane and a hclust dendrogram is drawn above the plane.

Usage

orditree3d(ord, cluster, prune = 0, display = "sites", choices = c(1, 2),
    col = "blue", text, type = "p", ...)
ordirgltree(ord, cluster, prune = 0, display = "sites", choices = c(1, 2),
    col = "blue", text, type = "p", ...)

Arguments

`ord`	An ordination object or an `ordiplot` object or any other structure defining a 2D plane.
`cluster`	Result of hierarchic cluster analysis, such as `hclust` or `agnes` or any other clutering that can be coerced to a compliant format by `as.hclust`.
`prune`	Number of upper levels hierarchies removed from the tree. If `prune` > 0, tree will be cut into `prune + 1` disconnected trees.
`choices`	Choice of ordination axes.
`display`	Ordination scores displayed.
`col`	Colour of tree. The colour can be a vector and it is used for the points, text and terminal branches. The colour of internal branches is a mixture of connected leaves.
`text`	Text to replace the default of item labels when `type = "t"`.
`type`	Display of leaves: `"p"` for points, `"t"` for text, and `"n"` for no display.
`...`	Arguments passed to `scores` and graphical functions.

Details

orditree3d uses scatterplot3d package to draw a static 3D plot of the dendrogram over the ordination, and ordirgltree uses rgl to make a dynamic, spinnable plot. The functions were developed to plot a cluster dendrogram over a 2D ordination plane, but any other plane can be used, for instance, a map.

Value

Function orditree3d returns invisibly a scatterplot3d result object amended with items points and internal that give the projected coordinates of ordination scores and internal nodes, and col.points and col.internal that give their colours. All matrix-like objects can be accessed with scores.

Function ordirgltree returns nothing.

Author(s)

Jari Oksanen.

Examples

data(dune, dune.env)
  d <- vegdist(dune)
  m <- metaMDS(d)
  cl <- hclust(d, "aver")
  orditree3d(m, cl, pch=16, col=cutree(cl, 3))
  ## ordirgltree makes ordinary rgl graphics. It accepts
  ## rgl.material() settings, and you can add elements to the
  ## open graph (for instance, bbox3d()).
  if (interactive() && require(rgl, quietly = TRUE)) {
  with(dune.env, ordirgltree(m, cl, col = as.numeric(Management), size = 6,
     lwd = 2, alpha = 0.6))
  }

vegan3d

Static and Dynamic 3D Plots for the 'vegan' Package

v1.1-2

GPL-2

Authors

Jari Oksanen [aut, cre], Roeland Kindt [aut], Gavin L. Simpson [aut]

Initial release

2018-10-25