michael watson (IAH-C)
2006-Mar-09 12:47 UTC
[R] Identifying or searching for labels in a hclust/dendrogram/heatmap
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 Many thanks Mick
Sean Davis
2006-Mar-09 13:01 UTC
[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 outMick, 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