shipunov (version 1.11)

Tcoords: Calculates coordinates of tips from 'hclust' plot

Description

Takes the 'hclust' plot and calculates coordinates of all tips

Usage

Tcoords(hcl, hang=0.1, add=0, horiz=FALSE)

Arguments

hcl

hclust object

hang

The fraction of the plot height by which labels should hang below the rest of the plot; better to make it equal to the 'hang' from hclust (default is 0.1).

add

Add to 'hang' to make labels look better; reliable value is about 0.03

horiz

Plot values for a horizontal tree?

Details

This function calculates coordinates for each tip of the plotted 'hclust' object. It is useful together with plot.hclust(..., labels=FALSE).

There are numerous applications of Tcoords(). Typical situation is when user wants to change default labels on plot.hclust() but it is possible only after conversion into the dendrogram. However, this conversion might alter the graphical representation, and, what is worse, is not suitable for advanced forms of plot.hclust(), for example, in 'pvclust' package or those from Bclust() or Jclust()-related commands.

Tcoords() allows to plot labels (or points, or any low lewel structures) separately. Therefore, it is possible to rotate them, colorize them, abbreviate them, change their font and so on. By default, labels will be plotted horizontally, not vertically as it is in plot.hclust().

To plot new labels in the same order, do not forget to apply the 'order' component of 'hclust' object (see below for the example).

Together with Hcoords(), it in principle allows to plot dendrogram in the alternative way (for example, with aid of segments() and text()). This possibility, however, needs a research.

See Also

hclust

Examples

# NOT RUN {
hcl <- hclust(UScitiesD, "ward.D2")
newlabels <- abbreviate(hcl$labels, 3)
newlabels <- newlabels[hcl$order] # do not forget to reorder labels!
plot(hcl, labels=FALSE)
text(Tcoords(hcl, add=0.03), newlabels, col=ifelse(grepl("W.D", newlabels), 2, 1))

## points instead of text labels
plot(hcl, labels=FALSE)
points(Tcoords(hcl), pch=19)

## how to colorize tips, useful if dendrogram is dense
iris.h <- hclust(dist(iris[, -5]))
plot(iris.h, labels=FALSE)
points(Tcoords(iris.h, add=0.01), col=iris$Species[iris.h$order]) # reorder lalels!

## can be used with Ploth(), i.e., with dendrogram
Ploth(hcl, labels=NA, horiz=TRUE) # hang=-1 is default
tc <- Tcoords(hcl, hang=-1, horiz=TRUE)
text(tc, newlabels, pos=4, xpd=TRUE)

# }