plotProfileDendrogram: Plot soil profiles below a dendrogram

In aqp: Algorithms for Quantitative Pedology

Plot soil profiles below a dendrogram

Description

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

Usage

plotProfileDendrogram(
  x,
  clust,
  rotateToProfileID = FALSE,
  scaling.factor = 0.01,
  width = 0.1,
  y.offset = 0.1,
  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	vertical scaling of the profile heights (may have to tinker with this)
width	scaling of profile widths
y.offset	vertical offset for top of profiles
dend.y.scale	extent of y-axis (may have to tinker with this)
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

You may have to tinker with some of the arguments to get optimal arrangement and scaling of soil profiles.

Author(s)

D.E. Beaudette

aqp documentation built on April 4, 2025, 4:15 a.m.