hyperSpec (version 0.98-20140523)

mark.dendrogram: 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.

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)