R help - Sep 2007 - side bars on dendrograms with latticeExtra

Dear all,

I am using the heatmap representations of latticeExtra package and I 
would be interested to draw color side bars representing the groups of a 
factor of interest. From my understanding of :

 > help(dendrogramGrob)
...
     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'.
...

I should use the argument add. Unfortunately I am not very familiar with 
'gpar' from grid package, and I cannot find the correct syntax to use 
this 'add' argument.

Does anyone has an example of how to draw side bars next to a dendrogram 
produced with latticeExtra?

Thank you,
Audrey

On 9/17/07, audrey <audrey at ebi.ac.uk> wrote:
> Dear all,
>
> I am using the heatmap representations of latticeExtra package and I
> would be interested to draw color side bars representing the groups of a
> factor of interest. From my understanding of :
>
>  > help(dendrogramGrob)
> ...
>      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'.
> ...
>
> I should use the argument add. Unfortunately I am not very familiar with
> 'gpar' from grid package, and I cannot find the correct syntax to
use
> this 'add' argument.
>
> Does anyone has an example of how to draw side bars next to a dendrogram
> produced with latticeExtra?
Here's one:


library(latticeExtra)

hc1 <- hclust(dist(USArrests, method = "canberra"))
hc1 <- as.dendrogram(hc1)
ord.hc1 <- order.dendrogram(hc1)
hc2 <- reorder(hc1, state.region[ord.hc1])
ord.hc2 <- order.dendrogram(hc2)

region.colors <- trellis.par.get("superpose.polygon")$col

levelplot(t(scale(USArrests))[, ord.hc2],
          scales = list(x = list(rot = 90)),
          colorkey = FALSE,
          legend           list(right                list(fun = dendrogramGrob,
                    args                     list(x = hc2, ord = ord.hc2,
                         side = "right", size = 10, size.add= 0.5,
                         add = list(rect                          list(col =
"transparent",
                              fill = region.colors[state.region])),
                         type = "rectangle"))))

-Deepayan