mark.dendrogram: Mark groups in 'hclust' dendrograms

In hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

Mark groups in hclust dendrograms

Description

Groups are marked by colored rectangles as well as by their levels.

Usage

mark.dendrogram(
  dendrogram,
  groups,
  col = seq_along(unique(groups)),
  pos.marker = 0,
  height = 0.025 * max(dendrogram$height),
  pos.text = -2.5 * height,
  border = NA,
  text.col = "black",
  label,
  label.right = TRUE,
  ...
)

Arguments

dendrogram	the dendrogram
groups	factor giving the the groups to mark
col	vector with colors for each group
pos.marker	top of the marker rectangle
height	height of the marker rectangle
pos.text	position of the text label
border	see text
text.col	color (vector) giving the color for the text markers
label	side label see example
label.right	should the side labels be at the right side?
...	handed to rect and text

Details

The dendrogram should be plotted separately, see the example.

Author(s)

Claudia Beleites

Examples

dend <- hclust (pearson.dist (laser[[]]))
par (xpd = TRUE, mar = c (5.1, 4, 4, 3)) # allows plotting into the margin
plot (dend, hang = -1, labels = FALSE)

## mark clusters
clusters <- as.factor (cutree (dend, k = 4))
levels (clusters) <- LETTERS [1 : 4]
mark.dendrogram (dend, clusters, label = "cluster")

## mark independent factor
mark.dendrogram (dend, as.factor (laser [,,405.36] > 11000),
pos.marker = -0.02, pos.text = - 0.03)

## mark continuous variable: convert it to a factor and omit labels
mark.dendrogram (dend, cut (laser [[,, 405.36]], 100), alois.palette (100),
                 pos.marker = -.015, text.col = NA,
                 label = expression (I [lambda == 405.36~nm]), label.right = FALSE)
 

hyperSpec documentation built on May 29, 2024, 7:28 a.m.