similar to: A question on stats::as.hclust.dendrogram

Hello, a. when I use hclust with the methods media, centroid, and mcquitty, and plot the results, the dendrograms have lines that are crossing each other. Is this ok? b. My next question refers to plot.dendrogram: How can I use parameters as "hang" or "cex" here? E.g. for st <- as.dendrogram(subtreeshc[[x]]) I would like to have something like this, where cex and hang

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

Dear R-Help, I have a clustering problem with hclust that I hope someone can help me with. Consider the classic hclust example: hc <- hclust(dist(USArrests), "ave") plot(hc) I would like to cut the tree up in such a way so as to avoid small clusters, so that we get a minimum number of items in each cluster, and therefore avoid singletons. e.g. in this example, you can see

Note that cophenetic.default (which works on the output of hclust(dist(X))) uses the row names of X as labels. as.dendrogram.hclust does not retain those row names so cophenetic.dendrogram cannot use them (so it orders them based on the topology of the dendrogram). Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, Apr 21, 2016 at 7:59 AM, William Dunlap <wdunlap at tibco.com> wrote:

Good afternoon, I ran heatmap and hclust on the same matrix x (strictly, I ran heatmap(x), and hclust(dist(t(x))), and realized that the two dendrograms were slightly different, in that the left-right arrangement of one pair of subclusters (columns) was reversed in the two functions (but all individual columns were grouped correctly). Looking through the code for heatmap as a most definite

I would like to be able to exert certain types of control over the plotting of dendrograms (representing hierarchical clusterings) that I think is best achieved by modifying the dendrogram object prior to plotting. I am using the "dendrogram" class and associated methods. Define the cluster number of each cluster formed as the corresponding row of the merge object. So, if you are

The problem: =========== Once a dendrogram has a branch with both a line type AND a color (which is a character color), the plot.dendrogram function will not plot and return an error. I say this is a bug because (I believe), we would like a dendrogram to be able to use character colors, while also allowing control over line types. This e-mail includes an example, and what I think a solution

I have tried to use rect.hclust() to draw a rectangle around a set of leaves, but am running into trouble. The rect.hclust() is drawing two rects instead of one, and of the wrong size: -------------------- scoreClusterObj <- hclust(scoreDistanceObj, method=clustMethod) order <- scoreClusterObj$order orderedLabels <- rep(0, length(order)) for (orderIndex in 1:length(order)) { # this

Dear I am using the 'as.dendrogram' function from the 'stats' library to convert from an hclust object to a dendrogram with a dataset of size ~30000 (an example code is below). I need the dendrogram structure to use the "dendrapply" and "attributes" functions and to access the child nodes, I do not need any of the plot properties. The problem is that it

Dear useRs, I am working on a project involving the clustering of a large dataset. I need to extract specific sub-clusters from the parent dendrogram for further analysis. The data is too large for the use of convenient tools such as identify.clust (it selects the specific group of interest on a graph), so alternatively I have saved the plot as a large image file so that it can be printed or

Dear All, How can the height of a leaf be extracted from a dendrogram? Sure, I can print it, but I am not able to, say, store it in an object. I think I understand that the height is a property of the split, not the leaf itself, but the printing functions display a "height" or "h" (which changes with "hang") and that is what I want. Obviously, the info is there

Hi all, Hi Gavin, thx for your help i finally found out what i want to do and how to fix it. just needed to get some more level my cut level was too small... two question remain... a) can i somehow scale the twigs after cutting ? b) how can i label the nodes and how to label which one... thx !! -m.

Is there any way to change the orientation of the labels on the end of the dendrograms to horizontal rather than vertical? If so, how can I do that. _____________________________________________ Patrick Richardson Biostatistician - Program of Translational Medicine Van Andel Research Institute - Webb Lab 333 Bostwick Avenue NE Grand Rapids, MI 49503 ph. 616.234.5787 This email message,

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

Hi, I was wondering if there is more flexibility in the output of dendrograms when plotting a hclust object. I can't seem to find information on how to change the default output of a "hanging" style tree with the axis on the right to a left-to-right plot with and axis on the bottom. Example code follows: library(vegan) #loads the "vegan" module that compuptes ANOSIM

Hi, I clustered a distance matrix and would like to draw it using plot.hclust or plot.dendrogram. The dendrogram is not informative because I have a few extremely small dissimilarities in the distance matrix (e.g. 0), but most of the other distances are in the range 1e10+-5000. I would like to show the tree only for the height of 1e10+-5000 but unfortunately their are no parameter like

Hi all, ok, i know i can cut a dendrogram, which i did. all i get is three objects that a dendrograms itself. for example: myd$upper, myd$lower[[1]], myd$lower[[2]] and so on. of course i can plot them seperately now. but the lower parts still have hundreds of branches. i?ll need a 30 " widescreen to watch the whole picture. what i?d like to is group the lower branches , so that i get a

Hi R helpers... I am having troubles because of the discrepancy between the dendrogram plotted from hclust and what is wrote in the hc2Newick file. I've got a matrix C: > hc <- hclust(dist(C)) > plot(hc) with the: > write(hc2Newick(hc),file='test.newick') both things draw completely different "trees"... I have also tried with the raw distance matrix D and

Hello, Is it possible to remove those extra margins on the "sample" axis from plot.dendrogram: par(oma=c(0,0,0,0),mar=c(0,0,0,0)) ddr<-as.dendrogram(hclust(dist(matrix(sample(1:1000,200),nrow=100)))) stats:::plot.dendrogram(ddr,horiz=F,axes=F,yaxs="i",leaflab="none") vs. stats:::plot.dendrogram(ddr,horiz=T,axes=F,yaxs="i",leaflab="none")

Dear r-list, I am trying to visually seperate the two main clusters of a dendrogram. The idea is to use: 'edgePar=list(lty=3)' for 'dend1[[1]]' and 'edgePar=list(lty=1)' for 'dend1[[2]]' I have not found a way to solve this. Any suggestions? Patrick hc <- hclust(dist(USArrests), "ave") (dend1 <- as.dendrogram(hc)) par(mfrow=c(2,2)) plot(dend1)