Mark groups in stats::hclust() dendrograms

Source: R/mark.dendrogram.R

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

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 graphics::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 graphics::rect() and graphics::text()

Details

The dendrogram should be plotted separately, see the example.

Author

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
)