Reproducing lattice dendrogram graph with ggplot2

Question

Is this possible to reproduce this lattice plot with ggplot2?

library(latticeExtra)
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",
                     size = 10))))

Answer 1

EDIT

From 8 August 2011 the ggdendro package is available on CRAN Note also that the dendrogram extraction function is now called dendro_data instead of cluster_data

---

Yes, it is. But for the time being you will have to jump through a few hoops:

1. Install the ggdendro package (available from CRAN). This package will extract the cluster information from several types of cluster methods (including Hclust and dendrogram ) with the express purpose of plotting in ggplot .
2. Use grid graphics to create viewports and align three different plots.

The code:

First load the libraries and set up the data for ggplot:

library(ggplot2)
library(reshape2)
library(ggdendro)

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

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

xx <- scale(mtcars)[col.ord, row.ord]
xx_names <- attr(xx, "dimnames")
df <- as.data.frame(xx)
colnames(df) <- xx_names[[2]]
df$car <- xx_names[[1]]
df$car <- with(df, factor(car, levels=car, ordered=TRUE))

mdf <- melt(df, id.vars="car")

Extract dendrogram data and create the plots

ddata_x <- dendro_data(dd.row)
ddata_y <- dendro_data(dd.col)

### Set up a blank theme
theme_none <- theme(
  panel.grid.major = element_blank(),
  panel.grid.minor = element_blank(),
  panel.background = element_blank(),
  axis.title.x = element_text(colour=NA),
  axis.title.y = element_blank(),
  axis.text.x = element_blank(),
  axis.text.y = element_blank(),
  axis.line = element_blank()
  #axis.ticks.length = element_blank()
)

### Create plot components ###    
# Heatmap
p1 <- ggplot(mdf, aes(x=variable, y=car)) + 
  geom_tile(aes(fill=value)) + scale_fill_gradient2()

# Dendrogram 1
p2 <- ggplot(segment(ddata_x)) + 
  geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) + 
  theme_none + theme(axis.title.x=element_blank())

# Dendrogram 2
p3 <- ggplot(segment(ddata_y)) + 
  geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) + 
  coord_flip() + theme_none

Use grid graphics and some manual alignment to position the three plots on the page

### Draw graphic ###

grid.newpage()
print(p1, vp=viewport(0.8, 0.8, x=0.4, y=0.4))
print(p2, vp=viewport(0.52, 0.2, x=0.45, y=0.9))
print(p3, vp=viewport(0.2, 0.8, x=0.9, y=0.4))

Answer 2

As Ben says, everything is possible. Some work to support dendrograms has been done. Andrie de Vries has made a fortify method of tree objects. However, the resulting graphic is not pretty as you can see.

The tile would be easy to do. For the dendrogram I would inspect plot.dendrogram (using getAnywhere ) to see how the coordinates for the segments are calculated. Extract those coordinates and use geom_segment to plot the dendrogram. Then use viewports to plot the tiles and the dendrogram together. Sorry I can't give a example, it's a lot of work and it's too late.

I hope this helps

Cheers

Answer 3

Doubtful. I do not see any functions in the Index for ggplot2 that would suggest support for dendrograms, and when this blogger put together a set of translations of the illustrations in Sarkar's Lattice book, he was unable to get a ggplot dendrogram legend:

http://learnr.wordpress.com/2009/08/10/ggplot2-version-of-figures-in-lattice-multivariate-data-visualization-with-r-part-9/

Answer 4

These links provide a solution for heatmaps with dendrograms in ggplot2:

https://gist.github.com/chr1swallace/4672065

https://github.com/chr1swallace/random-functions/blob/master/R/ggplot-heatmap.R

and also this one:

Align ggplot2 plots vertically