[R] coloring leaves in a hclust or dendrogram plot [solved]

[Gabor Grothendieck]

Where does one find A2Rplot that is called in that example?

A2R does not appear to be on CRAN.  I did find this:

  http://addictedtor.free.fr/Download/A2R.zip

which is a zip file containing some R code but it is not a package,
which the line library(A2R) seems to need, and it does not include
A2Rplot in any case.

On 3/10/06, Christos Hatzis <christos at silicoinsights.com> wrote:
> See also the colored dendrogram in the R Graph Gallery.  It has a couple of
> additional cool features.
>
> http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=79
>
>
> -Christos Hatzis
>
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Dylan Beaudette
> Sent: Friday, March 10, 2006 4:37 PM
> To: r-help at stat.math.ethz.ch
> Subject: Re: [R] coloring leaves in a hclust or dendrogram plot [solved]
>
> On Thursday 09 March 2006 06:12 pm, Dylan Beaudette wrote:
> > Greetings,
> >
> > I have perused the r-help mailing list archives for an answer to this
> > question, without avail.
> >
> > I would like to color the "leaves" of a dendrogram plot based on a
> > cutoff in one of the variables involved in the initial clustering.
> >
> > My input data is in the form of:
> >                   B         K
> > Alameda   0.2475770 0.7524230
> > Alpine    0.4546784 0.5453216
> > Amador    0.6278610 0.3721390
> >
> > essentially rows labeled by county name, with two variables: percent
> > voted for B and percent voted for K. While it is obvious that this is
> > somewhat of a contrived example, I intend to use this as a learning
> device.
> >
> > Here is the code used to create and plot the dendrogram:
> > hc <- hclust(dist(y), "ave")
> > dend <- as.dendrogram(hc)
> > plot(dend, main="CA 2004 Election Results by County")
> >
> > An example of the output can be found here:
> > http://casoilresource.lawr.ucdavis.edu/drupal/node/206?size=_original
> >
> >
> > I have experimented with the edgePar and nodePar parameters for the
> > plot.dendrogram() method, but have not been able to make sense of the
> > output.
> >
> > The basis for setting the colors of the leaves in the dendrogram is a
> > simple majority calculation:
> >
> > reds <- y[y$B > 0.5, ]
> > blues <- y[y$K > 0.5, ]
> >
> > Such that leaves in the tree will be colored based on the membership
> > in either of the two above groups.
> >
> > Is there a resource documenting how this might be accomplished?
> >
> > Any thoughts or ideas would be greatly appreciated.
> >
> > Cheers,
> >
> > Dylan
>
> Replying to my own post...
>
> Discovered the dendapply() function:
>
> reds <<- as.factor(row.names(y[y$B > 0.5, ])) blues <<-
> as.factor(row.names(y[y$K > 0.5, ]))
>
> #define a function for coloring and sizing node elements:
> colLab <- function(n)
>  {
>  if(is.leaf(n))
>    {
>    a <- attributes(n)
>    if ( length(which(blues == a$label)) == 1 )
>      {
>      attr(n, "nodePar") <- c(a$nodePar, list(lab.col = "blue", lab.cex=.7,
> col="blue", cex=pop[n], pch=16 ))
>      }
>    else
>      {
>      attr(n, "nodePar") <- c(a$nodePar, list(lab.col = "red", lab.cex=.7,
> col="red", cex=pop[n], pch=16))
>      }
>    }
>  n
>  }
>
> #modfiy dendrogram nodes and re-plot
> dend_colored <- dendrapply(dend, colLab)
>
> ...which did the trick
>
> http://casoilresource.lawr.ucdavis.edu/drupal/node/210
>
>
>
> --
> Dylan Beaudette
> Soils and Biogeochemistry Graduate Group University of California at Davis
> 530.754.7341
>
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