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:[EMAIL PROTECTED] > 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)" <[EMAIL PROTECTED]> > 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 > > ______________________________________________ > R-help@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@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