plotProfileDendrogram: Plot soil profiles below a dendrogram or cladogram

In aqp: Algorithms for Quantitative Pedology

Plot soil profiles below a dendrogram or cladogram

Description

Plot soil profiles below a dendrogram, using methods from the ape package.

Usage

plotProfileDendrogram(
  x,
  clust,
  rotateToProfileID = FALSE,
  scaling.factor = 5 * mean(clust$height)/max(x),
  width = 0.25,
  y.offset = 60 * mean(clust$height)/max(x),
  dend.y.scale = max(clust$height * 2, na.rm = TRUE),
  dend.color = par("fg"),
  dend.width = 1,
  dend.type = c("phylogram", "cladogram"),
  debug = FALSE,
  ...
)

Arguments

x	a SoilProfileCollection object
clust	a hierarchical clustering object generated by hclust(), cluster::agnes(), or cluster::diana()
rotateToProfileID	logical, attempt rotation of dendrogram according to original profile IDs, requires dendextend package
scaling.factor	numeric, vertical scaling of the profile heights (default estimate printed if not specified)
width	numeric, scaling of profile widths
y.offset	numeric, vertical offset for top of profiles (default estimate printed if not specified)
dend.y.scale	numeric, scaling of dendrogram (default estimate printed if not specified)
dend.color	dendrogram line color
dend.width	dendrogram line width
dend.type	dendrogram type, passed to plot.phylo(), either "phylogram" or "cladogram"
debug	logical, optionally print debugging data and return a data.frame of linking structure
...	additional arguments to plotSPC()

Value

This function is typically called to create graphical output, when debug = TRUE a data.frame of IDs and linking structure used to build the figure.

Note

The default values of scaling.factor, y.offset, and dend.y.scale are based on clust$height and max(x), and should be close to optimal. Use the defaults as a starting point for finer control.

Author(s)

D.E. Beaudette

aqp documentation built on Jan. 17, 2026, 9:07 a.m.