R help - Nov 2008 - Rendering Dendrograms

Hello all
I've been using the hclust and as.dendrogram objects for hierarchical
 clustering. The problem I have is that my sample set is now so large (circa
 500 points) that it isn't possible to view the leaf nodes.

 I'd like to be able to zoom in on specific areas of the graph by selecting 
a
 region with the mouse.  I've deduced from trial and error that the xlim and
 ylim parameters don't work with these plots and the only method I've
had
any
 success with is to cut the tree at a specific point and display the lower
 region.  However, the cut function returns a list of all subtrees below the
 specified height and I have no way of selecting a particular subtree (that
 is, cutting on the x-axis).

The identify and rect.hclust functions seem to do this OK  and  in fact 
these
 partially solve my problem but I want to use getGraphicsEvent() if possible
 since this also allows interaction with the keyboard (so that I can use the
 backspace key for example to return to the previous plot). I'm fairly new 
to
 R so may be wrong but it appears that the plots are single threaded and can
 respond to either a set of graphics events or an identify loop but not 
both)

 It has been suggested that I look at  Graphviz since this has more
 comprehensive mapping facilities. Is this likely to help? Is there for
 example a method for converting an R hclust object to an Graphviz ICLUST or
 some alternative method for describing an hclust in the Graphviz .DOT
 notation?

 Or can anybody suggest an alternative approach ??

 Regards

 Mark

>
>
>

Hi Mark,

similar questions were at least two times during the last weeks, see

http://tolstoy.newcastle.edu.au/R/e5/help/08/11/6722.html

http://tolstoy.newcastle.edu.au/R/e5/help/08/11/6736.html

or

http://tolstoy.newcastle.edu.au/R/e5/help/08/11/7790.html

or search the archives yourself:

http://tolstoy.newcastle.edu.au/R/

search for "cluster graph" or "plot.hclust"


Thomas P.


Mark Cook wrote:
> 
> 
> 
> Hello all
> I've been using the hclust and as.dendrogram objects for hierarchical
> clustering. The problem I have is that my sample set is now so large (circa
> 500 points) that it isn't possible to view the leaf nodes.
> 
> I'd like to be able to zoom in on specific areas of the graph by 
> selecting a
> region with the mouse.  I've deduced from trial and error that the xlim
and
> ylim parameters don't work with these plots and the only method
I've had
> any
> success with is to cut the tree at a specific point and display the lower
> region.  However, the cut function returns a list of all subtrees below the
> specified height and I have no way of selecting a particular subtree (that
> is, cutting on the x-axis).
> 
> The identify and rect.hclust functions seem to do this OK  and  in fact 
> these
> partially solve my problem but I want to use getGraphicsEvent() if possible
> since this also allows interaction with the keyboard (so that I can use the
> backspace key for example to return to the previous plot). I'm fairly 
> new to
> R so may be wrong but it appears that the plots are single threaded and can
> respond to either a set of graphics events or an identify loop but not 
> both)
> 
> It has been suggested that I look at  Graphviz since this has more
> comprehensive mapping facilities. Is this likely to help? Is there for
> example a method for converting an R hclust object to an Graphviz ICLUST or
> some alternative method for describing an hclust in the Graphviz .DOT
> notation?
> 
> Or can anybody suggest an alternative approach ??
> 
> Regards
> 
> Mark
> 
> 
>>
>>
>>
> 
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