similar to: plotting dendrograms from cluster analyses

Hi all, Can someone tell me how to justify (right or left) the labels on the branches of a dendrogram tree? I have produced a dendrogram via agnes and plotted it with pltree. The dendrogram terminal branch labels seem to be centre-justified by default and I was hoping to change this to left justification. Thanks, Duncan ***************************************** Dr. Duncan Mackay School of

I'd like to be able to cut dendrograms at a height I specify and then plot the resulting subtrees. I wanted to use the dendrogram object for this purpose because there doesn't seem to be a canned way to cut a hclust object and get a list of hclust objects, but there is a function (cut) that does that for dendrograms. The problem I'm having is that when I plot a dendrogram, I

Hello, I've been clustering my data using hclust and cutting the resulting tree with cutree. Separately, I visualize the clusterings with heatmap. Is it possible to have the dendrogram on the heatmap reflect the cutree results? That is, instead of having one large dendrogram, it would have 4 or 25 in the example below. Any guidance on if that's possible or not, and what kinds of

When I use the function cutree(), the numbers of the clusters are not in the same order as the plotted dendrogram. Is there any way of sorting them so that they match the tree? Is it possible to plot a dendrogram horizontally, preferably with the branches to the right? This would enable some practical composite plots, e.g. labels that were an entire table with several columns of information, or

Hello all, I am using libraries (mva,cluster) to produce dendrograms. With 1000 examples the dendrogram gets too crowded, and i am wondering whether there is an option (which i cannot find) to set the number of leaf nodes, like in matlab, and return the plot and the assignment map examples -> leaf nodes. Any suggestion is appreciated. Thanks Edo

I'm clustering rather large data sets and would like to cut the dendrograms to get a better view of specific components. I calculate the dissimilarity matrix using daisy() because I have a mixture of variable types: factors, ordered factors and numerical variables. If I want one dendrogram, I use agnes() for the agglomerative nesting and pltree() to draw the dendrogram. That way, I get the

Ladies and Gentlemen, As Johan Lindberg points out, the documentation for handling dendrograms is sparse....Does anyone know who is responsible for or working on development of tree methods and objects? I've written a couple of scripts for my own use to translate between parenthetical (A(B(CD))) or binary A00 B10 C11 D11 tree formats and cluster objects in R, but as an inexperienced

> I have performed clustering analysis with hclust (Ward's method) on a > database of 800 samples. As you may imagine the full dendrogram is not > really readable. I have obtained groups with cutree. I would like to plot > sub-sections of my big dendrogram to show group 1, group 2 and so on. I don't think R has anything like subtree in Splus, unfortunately. I think what has

Dear R-helpers, I have 4-dimensional atmospheric data (x,y,z,t), which I want to analyse on spatio-temporal diversities. As far as I understand there only exists the possibility to construct time series as two-dimensional matrices (mts). For the moment, I hold it in different objects: 1. a four-dimensional array for the spatial related analyses 2. a two-dimensional mts timeserie, which was

Hello R-Helpers, I have a question about extracting the clusters of genes after we make the heatmap (say ht4) using the heatmap.2 function. Basically, I want to get the clusters which are shown as row dendrogram in the heatmap. I understand that ht4$rowDendrogram is an object of dendrogram and it containes details of all the nodes and branches, but lets say I want to know the number of clusters

Dear R user, I am a biochemist/bioinformatician, at the moment working on protein clusterings by conformation similarity. I only started seriously working with R about a couple of months ago. I have been able so far to read my way through tutorials and set-up my hierarchical clusterings. My problem is that I cannot find a way to obtain information on the rooting of specific nodes, i.e. of

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

Hi, this is rather a (presumed) bug report than a question because I can solve my personal statistical problem by working with hclust instead of agnes. I have done a complete linkage clustering on a dist object dm with 30 objects with agnes (R 1.8.0 on RedHat) and I want to obtain the partition that results from a cut at height=0.4. I run > cl1a <- agnes(dm, method="complete")

Hi, this is rather a (presumed) bug report than a question because I can solve my personal statistical problem by working with hclust instead of agnes. I have done a complete linkage clustering on a dist object dm with 30 objects with agnes (R 1.8.0 on RedHat) and I want to obtain the partition that results from a cut at height=0.4. I run > cl1a <- agnes(dm, method="complete")

Hello all, A question/suggestion: I was wondering if there is a chance of changing stats::cutree to be S3 and use cutree.hclust? For example: cutree <- function(tree, k = NULL, h = NULL,...) { UseMethod("cutree") } cutree.hclust <- stats::cutree # This will obviously need the actual content of stats::cutree This would be nicer for people like me to add new methods to

Thanks a lot, Michael! I cc to R-help, where this question really belongs {as the 'Subject' suggests itself...} -- please drop 'bioconductor' from CC'ing further replies. >>>>> "michael" == michael watson (IAH-C) <michael.watson at bbsrc.ac.uk> >>>>> on Thu, 17 Jun 2004 09:16:59 +0100 writes: michael> OK, admittedly it

Hi! In the example: hc <- hclust(dist(USArrests), "ave") dend1 <- as.dendrogram(hc) dend2 <- cut(dend1, h=70) Do the branches "Branch 1", "Branch 2", "Branch 2"...in dend2$upper str(dend2$upper) --[dendrogram w/ 2 branches and 4 members at h = 152] |--[dendrogram w/ 2 branches and 2 members at h = 77.6] | |--leaf "Branch 1" (h=

Hi, I have submitted a package to CRAN in ftp://ftp.tuwien.ac.at/incoming/pastecs_1.0.tar.gz. The R extension manual advises to send a mail to cran at ci.tuwien.ac.at about it, but it fails. I have also tried WWWadmin at ci.tuwien.ac.at. Are these email adresses still valid? Best, Philippe Grosjean ...........]<(({?<...............<?}))><............................... ) ) ) )

Hello all, would someone please tell me why the following code doesn't "work" (i.e. do what i expected!). I wanted to convert numeric variables in a matrix to ordered (for input as nominal variables into the 'daisy' program). Why does the following code seem to work, but the "is.ordered" command reports that the variables are not ordered (factors)?? > xxx <-

I stumbled across this link and was wondering if this has any relation to the R project. http://www.fas.umontreal.ca/BIOL/Casgrain/en/labo/R/index.html -jennifer ----------------------------------- J. Steinbachs, Ph.D. Computational Biologist http://compbiology.org ----------------------------------- -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing