similar to: Finding an order for an hclust (dendrogram) object without intersections

Hello all, I'm now working with hclust objects and was hoping to perform some basic editing on them like: - Joining = the merging of two hclust objects (so they will share one root) - Splicing = So to cut/extract a branch out of an hclust object - that by itself will be an hclust object. I noticed I could extract one element of an hclust object by turning it into a dendrogram,

Hello all, I wish to compare two dendrograms (representing Hierarchical Clusterings). My problems are several: 1) how do I manually create a dendrogram object ? That is, how can I reconstruct it as an "hclust" object that creates such a dendrogram, when all I have is the dendrogram image (but don't have the underlaying distance matrix that produced it) ? I see that there is a

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

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:

Hi all, This is the first time I'm writing to R-devel, and this time I'm just asking for the purpose for a certain line of code in stats::as.hclust.dendrogram, which comes up as I'm trying to fix dendextend. The line in question is at line 128 of dendrogram.R in R-3.3.3, at stats::as.hclust.dendrogram: stopifnot(length(s) == 2L, all( vapply(s, is.integer, NA) )) Is there any

I want to change leaf color by group in hclust plot. I've seen several answers about A2R package but I cannot install A2R and Rtools in windows. Do you know how to install A2R package in windows or how to change leaf color by group in hclust plot? Thank you in advance, Soyeon

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

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

plot.hclust: Setting up a window for a dendrogram assumes the first link is the shortest and the last is the longest. This is not always the case when the clustering was done with hclust, method="median" or method="centroid", and the dendrogram sometimes doesn't fit within the window. I propose the fix listed below. src/main/ --- plot.c Wed Sep 17 01:03:39 2003 +++

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

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, 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

?hclust listed several references. I'm wondering what is the best resource that explained clustering algorithms, dendrogram and various clustering algorithms that are implemented in R. Thank you!

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

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

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

Hello dear R-help mailing list members, I wish to create an hclust object which will be based on a customized hierarchical clustering algorithm, programmed in R. After looking into the hclust function, I noticed that the algorithms themselves are implemented in Fortran. In order for me to implement my algorithm in R, it would be very helpful if there was some example of implementing (even one

I've been trying to get plot.hclust to work with a hclust object I created and have not had much success. It seems that there is some "hidden" characteristic of a hclust object that I can't see. This is most easily seen in the following example, where plot.hclust works on one object, but when this object is "dumped" and then re-read, plot.hclust no longer works. Is

Hi all, I've been doing some investigation to see if it is possible to implement an hclust/dendrogram related requirement that I've been given. So far ?hclust and a lot of googling haven't provided the information I'm looking for (I've been using R sporadically for a year). The requirement I have is to: On a dendrogram plot, draw points at various merge locations, based on

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