dendrogramGrob: Create a Grob Representing a Dendrogram

In latticeExtra: Extra Graphical Utilities Based on Lattice

Description

This function creates a grob (a grid graphics object) that can be manipulated as such. In particular, it can be used as a legend in a lattice display like levelplot to form heatmaps.

Usage

dendrogramGrob(x, ord = order.dendrogram(x),
               side = c("right", "top"),
               add = list(), size = 5, size.add = 1,
               type = c("rectangle", "triangle"),
               ...)

Arguments

x	An object of class "dendrogram". See dendrogram for details
ord	A vector of integer indices giving the order in which the terminal leaves are to be plotted. If this is not the same as order.dendrogram(x), then the leaves may not cluster together and branches of the dendrogram may intersect.
side	Intended position of the dendrogram when added in a heatmap. Currently allowed positions are "right" and "top".
add	Additional annotation. Currently, it is only possible to add one or more rows of rectangles at the base of the dendrogram. See details below.
size	Total height of the dendrogram in "lines" (see unit)
size.add	Size of each additional row, also in "lines"
type	Whether a child node is joined to its parent directly with a straight line ("triangle") or as a “stair” with two lines ("rectangle")
...	Extra arguments. Currently ignored.

Details

The add argument can be used for additional annotation at the base of the dendrogram. It should be a list with one component for each row, with names specifying the type of annotation and components specifying the contents. Currently, the only supported name is "rect" (which can be repeated), producing rectangles. The components in such a case is a list of graphical parameters, possibly vectorized, that are passed on to gpar.

Value

An object of class "grob"

Author(s)

Deepayan Sarkar [e-mail]

See Also

heatmap, levelplot

Examples

data(mtcars)
x  <- t(as.matrix(scale(mtcars)))
dd.row <- as.dendrogram(hclust(dist(x)))
row.ord <- order.dendrogram(dd.row)

dd.col <- as.dendrogram(hclust(dist(t(x))))
col.ord <- order.dendrogram(dd.col)

library(lattice)

levelplot(x[row.ord, col.ord],
          aspect = "fill",
          scales = list(x = list(rot = 90)),
          colorkey = list(space = "left"),
          legend =
          list(right =
               list(fun = dendrogramGrob,
                    args =
                    list(x = dd.col, ord = col.ord,
                         side = "right",
                         size = 10)),
               top =
               list(fun = dendrogramGrob,
                    args =
                    list(x = dd.row, 
                         side = "top",
                         type = "triangle"))))


## Version with unsorted rows.

## For illustration, MPG ploted again at foot of dendrogram

mpg <- x["mpg", col.ord]
mpg.col <- level.colors(mpg, at = do.breaks(range(mpg), 10),
                        col.regions = terrain.colors)

levelplot(x[, col.ord],
          aspect = "iso",
          scales = list(x = list(rot = 90)),
          colorkey = FALSE,
          legend =
          list(right =
               list(fun = dendrogramGrob,
                    args =
                    list(x = dd.col, ord = col.ord,
                         side = "right",
                         add = list(rect = list(fill = mpg.col)),
                         size = 10)),
               top =
               list(fun = dendrogramGrob,
                    args =
                    list(x = dd.row, ord = sort(row.ord),
                         side = "top", size = 10,
                         type = "triangle"))))

latticeExtra documentation built on Sept. 19, 2020, 3:01 p.m.