Tcoords: Calculates coordinates of tips from 'hclust' plot

In shipunov: Miscellaneous Functions from Alexey Shipunov

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; the 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().

Tcoords() treats labels in order of their appearance on the dendrogram and not in their initial order, so do not forget to apply the 'order' component of 'hclust' object (see below for examples).

Together with Hcoords(), Tcoords() in principle allows to plot dendrogram in the alternative way (for example, with aid of segments() and text()). That will allow, for example, to plot 'hclust' horizontally without conversion into dendrogram. This possibility, however, reqiures a further research.

Please also see Fence() and Tctext() which are convenient functions based on Tcoords() for adding segments and text labels, respectively.

See Also

hclust, Ploth, Fence, Tctext

Examples

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, cex=1.1) # Ploth() cannot change text size

shipunov documentation built on Feb. 16, 2023, 9:05 p.m.