similar to: Cannot allocate memory block

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

Thanks to Andy and Thomas, Reading help(hclust) more carefully would have done it but sometimes you do not see the wood for the trees... So hc$merge does exactly what I want. I have never been aware of the command str to get the structure of an R-object. It seems pretty useful to me. Thanks, Arne > -----Original Message----- > From: Liaw, Andy [mailto:andy_liaw at merck.com] >

Hello, I'm having trouble figuring out how to see resulting groups (clusters) from my hclust() output. I have a very large matrix of 4371 plots and 29 species, so simply looking at the graph is impossible. There must be a way to 'print' the results to a table that shows which plots were in what group, correct? I've attached the matrix I'm working with (the whole thing

I am using hclust and plot to produce dendrograms. Using my input data I am able to complete an analysis and obtain a vertical plot. I want to be able to plot the dendrogram horizontally.I am using version 2.6 of R and have updated my packages recently. Using the sample script for dendrograms I can produce a horizontal plot using the instruction horiz = TRUE in plot(). When I use the same

library(mva) data(USArrests) hc <- hclust(dist(USArrests), "ave") plot(hc) # OK dump(c("hc"), "tst") rm(hc) source("tst") plot(hc) # Error in plot.hclust(hc) : invalid dendrogram input The same problem occurs with dput/dget --please do not edit the information below-- Version: platform =

Buenas tardes a todos, Estoy interesado en cambiar los límites del eje y en un dendograma construído utilizando la función hclust(). A continuación un ejemplo: hc <- hclust(dist(USArrests), "ave") plot(hc) Hasta aquí todo bien. Si quisiera cambiar los límites del eje "y" de c(0, 200)? Al usar plot(hc, ylim = c(0, 200)) no observo efecto alguno. Qué puedo hacer?

Dear R-users, I tried to receive the merge details of a clustering by using the summary function of hclust. For illustration I use the Longley data as done by Prof Ripley (Wed 11 Apr 2001) d <- dist(longley.y) d <- d/max(d) hc <- hclust(d, "ave") But instead of getting a matrix for $merge I get: >summary(hc) Length Class Mode merge 30 -none- numeric

I have a large excel file with data in it. I converted it to a 'csv' format. I imported this dataset to R using the follownig command mldata <- read.csv("c:\\temp\\mldata.csv", header=T) all the column names and the rows seems to be correct. Now that I have this object, I need to perfrom hclust. I used the following hc <- hclust(dist(mldata), method="single")

Hi, I am new to clustering in R and I have a dataset with approximately 17,000 rows and 8 columns with each data point a numerical character with three decimal places. I would like to cluster the 8 columns so that I get a dendrogram as an output. So, I am simply creating a distance matrix of my data, using the 'hclust' function, and then plotting the results (see below, my data is

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

Hello everyone, Does anyone know how to implement the argument "unit" in R's plclust function ? I used to use Splus where this argument exists but it has not been implemented in R's plclust. The reason why I switched from Splus to R is that Ward's method is not implemented for S's hclust whereas it is implemented for R's hclust. What I would need is S's plclust

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

Hi I have a distance matrix which is computed by user defined method. I would like to plot the dendrogram. I would like to use different color and want the leaves laying down bottom. The script like this. I am not familiar with R. I followed the example shown in http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dendrogram.html dist.obj <- as.dist(matrix.distance) hc.obj <-

I am doing cluster analysis [hclust(Dist, method="average")] on data that potentially contains redundant objects. As expected, the inclusion of redundant objects affects the clustering result, i.e., the data a1, = a2, = a3, b, c, d, e1, = e2 is likely to cluster differently from the same data without the redundancy, i.e., a1, b, c, d, e1. This is apparent when the outcome is visualized

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:

Hello, I have been using the "cophenetic" function for objects of class "dendrogram" and I have realised that it gives different results when it is used with objects of class "hclust". For instance, running the first example in the help file of the "cophenetic" function, d1 <- dist(USArrests) hc <- hclust(d1, "ave") d2 <-

Hello to all, I still have this doubt. I'd like to colour the different labels of my dendrogram each one with a different colour. How can I do? I guess I could do using *edgetext* and then *t.col* or* lab.col* but I don't know how to add edgetext to my dendrogram. Can you help me please? Example: require(graphics); require(utils) hc <- hclust(dist(USArrests), "ave") (dend1

Dear All According to the identify.hclust documentation the function "cuts the tree at the vertical position of the pointer and highlights the cluster containing the horizontal position of the pointer". When I carry out this, the tree isn't cut where I click - in fact, there seems to be a limit below which I cannot go. Consider the following code: mat <- matrix(rnorm(5000),

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, I have a gene expression experiment with 20 samples and 25000 genes each. I'd like to perform clustering on these. It turned out to become much faster when I transform the underlying matrix with t(matrix). Unfortunately then I'm not anymore able to use cutree to access individual clusters. In general I do something like this: hc <- hclust(dist(USArrests), "ave")