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

[Christos Hatzis]

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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