[R] Identifying or searching for labels in a hclust/dendrogram/heatmap
ligges at statistik.uni-dortmund.de
Fri Mar 10 09:41:12 CET 2006
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
> Any suggestions?
> 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>
>>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
> 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.
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