plotProfileDendrogram: 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,
  ...
)

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.

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()

Author

D.E. Beaudette