monoClust (version 1.2.1)

plot.MonoClust: Plot MonoClust Splitting Rule Tree

Description

Print the MonoClust tree in the form of dendrogram.

Usage

# S3 method for MonoClust
plot(
  x,
  uniform = FALSE,
  branch = 1,
  margin = c(0.12, 0.02, 0, 0.05),
  minbranch = 0.3,
  text = TRUE,
  which = 4,
  stats = TRUE,
  abbrev = c("no", "short", "abbreviate"),
  digits = getOption("digits") - 2,
  cols = NULL,
  col.type = c("l", "p", "b"),
  rel.loc.x = TRUE,
  show.pval = TRUE,
  ...
)

Arguments

x

MonoClust result object.

uniform

If TRUE, uniform vertical spacing of the nodes is used; this may be less cluttered when fitting a large plot onto a page. The default is to use a non-uniform spacing proportional to the inertia in the fit.

branch

Controls the shape of the branches from parent to child node. Any number from 0 to 1 is allowed. A value of 1 gives square shouldered branches, a value of 0 give V shaped branches, with other values being intermediate.

margin

An extra fraction of white space to leave around the borders of the tree. (Long labels sometimes get cut off by the default computation).

minbranch

Set the minimum length for a branch to minbranch times the average branch length. This parameter is ignored if uniform = TRUE. Sometimes a split will give very little improvement, or even no improvement at all. A tree with branch lengths strictly proportional to improvement leaves no room to squeeze in node labels.

text

Whether to print the labels on the tree.

which

Labeling modes, which are:

• 1: only splitting variable names are shown, no splitting rules.

• 2: only splitting rules to the left branches are shown.

• 3: only splitting rules to the right branches are shown.

• 4 (default): splitting rules are shown on both sides of branches.

stats

Whether to show statistics (cluster sizes and medoid points) on the tree.

abbrev

Whether to print the abbreviated versions of variable names. Can be either "no" (default), "short", or "abbreviate". Short forms of them can also be used.

If "no", the labels recorded in x$labels are used.

If "short", variable names will be turned into "V1", "V2", ...

If "abbreviate", abbreviate() function will be used. Use the optional arguments for this function.

digits

Number of significant digits to print.

cols

Whether to shown color bars at leaves or not. It helps matching this tree plot with other plots whose cluster membership were colored. It only works when text is TRUE. Either NULL, a vector of one color, or a vector of colors matching the number of leaves.

col.type

When cols is set, choose whether the color indicators are shown in a form of solid lines below the leaves ("l"), or big points ("p"), or both ("b").

rel.loc.x

Whether to use the relative distance between clusters as x coordinate of the leaves. Default is TRUE.

show.pval

If MonoClust object has been run through perm.test(), whether to show p-value on the tree.

...

Arguments to be passed to graphics::plot.default() and graphics::lines().

Value

A plot of splitting rule.

Examples

# NOT RUN {
library(cluster)
data(ruspini)

# MonoClust tree
ruspini4sol <- MonoClust(ruspini, nclusters = 4)
plot(ruspini4sol)
# }
# NOT RUN {
# MonoClust tree after permutation test is run
ruspini6sol <- MonoClust(ruspini, nclusters = 6)
ruspini6_test <- perm.test(ruspini6sol,
                           data = ruspini,
                           method = "sw",
                           rep = 1000)
plot(ruspini6_test, branch = 1, uniform = TRUE)
# }