latticeExtra: dendrogramGrob – R documentation

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dendrogramGrob

Create a Grob Representing a Dendrogram

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 deepayan.sarkar@r-project.org

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

Extra Graphical Utilities Based on Lattice

v0.6-29

GPL (>= 2)

Authors

Deepayan Sarkar <deepayan.sarkar@r-project.org>, Felix Andrews <felix@nfrac.org>

Initial release

2019-12-18