[R] Identifying or searching for labels in a hclust/dendrogram/heatmap

[Uwe Ligges]

michael watson (IAH-C) wrote:

> Hi Sean
>  
> Thanks for the help, but I really wanted to do this in R :)


Not sure whether it works for your example, but perhaps you will find 
Klimt useful:
http://stats.math.uni-augsburg.de/Klimt/

Uwe Ligges


> Any suggestions?
>  
> Mick
> 
> ________________________________
> 
> From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
> Sent: Thu 09/03/2006 1:01 PM
> To: michael watson (IAH-C); r-help
> Subject: Re: [R] Identifying or searching for labels in a hclust/dendrogram/heatmap
> 
> 
> 
> 
> 
> 
> On 3/9/06 7:47 AM, "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk>
> wrote:
> 
> 
>>Hi
>>
>>Sorry if this is in the help :-S
>>
>>I've looked at example(dendrogram) and though it gives some indication of what
>>I want, it doesn't do all.
>>
>>OK, so here is what I want to do: draw a tree, and then have an action, on
>>user-click, to either draw a sub tree or a plot of the data.  I also want
>>users to be able to search for a particular label and have it highlighted on
>>the tree, say in red, where all the other labels are black.
>>
>>Now, the only tree I can use the "user-click" with is an hclust object, with
>>the identify.hclust() function.  As far as I know, neither the dendrogram
>>objects or the output of heatmap is cut-able in this way.  So I have the
>>sub-tree and plot drawing set up on user-click using an hclust object and
>>identify.hclust - good :)
>>
>>Therefore I am working with hclust objects (which is a shame as the dendrogram
>>and heatmap objects look prettier) but I can cope.  How do I then go on and
>>highlight a single label, or group of labels, when I have plotted the hclust
>>object?  Can I highlight labels on dendrograms and heatmaps 2?
>>
>>I can just imagine that after a user has drawn the tree, they will want to
>>know where their genes of interest actually lie within that tree.
>>
>>I'm happy to share the completed code when I have sorted all of this out
> 
> 
> Mick,
> 
> I personally would make use of the ctc package (bioconductor) to output data
> to Treeview (and/or cluster).  R may be able to do this, but interaction
> with graphics still leaves a bit to be desired in R (at least as compared to
> a dedicated, specialized Java App), particularly once you get beyond about
> 50 genes.  Treeview is just much better set up for this kinda stuff.  You
> could probably automate the process given, for example, a limma MAList or
> fit object, or something like that.
> 
> That said, I'd love to see what other people come up with to accomplish what
> you are asking.
> 
> Sean
> 
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