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Dylan Beaudette

2006-Mar-10 02:12 UTC

[R] coloring leaves in a hclust or dendrogram plot

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






-- 
Dylan Beaudette
Soils and Biogeochemistry Graduate Group
University of California at Davis
530.754.7341

Dylan Beaudette

2006-Mar-10 21:36 UTC

head link

[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

Christos Hatzis

2006-Mar-10 21:49 UTC

head link

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

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

______________________________________________
R-help at stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

Gabor Grothendieck

2006-Mar-11 14:56 UTC

head link

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

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
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>

R help - Mar 2006 - coloring leaves in a hclust or dendrogram plot

[R] coloring leaves in a hclust or dendrogram plot

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

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

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