Plot soil profiles below a dendrogram — plotProfileDendrogram • aqp

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

D.E. Beaudette