similar to: Node colors in pvclust

Hi, I am new to clustering and was wondering why pvclust using "maximum" as distance measure nearly always results in p-values above 95%. I wrote an example programme which demonstrates this effect. I uploaded a PDF showing the results Here is the code which produces the PDF file: ------------------------------------------------------------------------------------- s <-

Dear All I'm using PVClust to perform hierarchical clustering, for the output plot I can control most of the graphical I need, however the plot is large and I would like to split it vertically into two panels one above the other. Is there a way to plot only part of a PVClust plot, I tried to convert it to a dendrogram with result2 = as.dendrogram(result) however I get the error message

Hi all, I'm new to R and I'm struggling to decipher an error message. Briefly, I am trying to use the pvclust package to do hierarchical clustering of some CGH data. The data is from the Progenetix CGH database. It is arranged as a table where each column is a single case and each row is a single chromosome band. The value in each cell is either 0, 1, 2, or -1. Corresponding to no change,

Hi all I am writing to you with a question regarding the pvclust package. And yes, before the usual people produce their usual contact-the-package-maintainers line, ye, I tried that but the emails one can find on the web either bounce or are not responded to. Also, yes, this error has already been reported as a bug but been shot down as not reproducible

Hello all, I posted a question to this list last week and received no response. I am unsure if this means no-one knows the answer or if I posed the question badly. I'm going to assume I posed the question badly and try again. I am new to R so it is quite likely it's a very naive question, however if there is something blindingly obvious that I am missing or if there is another resource I

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

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, I am a new R user and have a question regarding dendrogram coloring. I would like to color each leaf in the dendrogram (dhc) according to a specific criterion. For me this criterion is the gene name. For this, I created a data.frame with 2 variables: The gene name and the corresponding color. Using the following function, adapted from "dendrapply {stats}", I still have the same

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

You should reply to the list, not just me, and even more because I cannot really help you!! My guess (but I don't know this package, and even less this function) is that pvclust() is expecting a matrix as the first argument. However, "cluster" is no data, it is a function. Why, I don't know. Take a closer look at ?pvclust, especially the "usage",

Dear all, I have been trying the following without avail and would be very grateful for any help. From a dendrogram (recursive list of lists with some structure), I would like to obtain some information of the component lists and of the enclosing list at the same time. In dendrogram-speech I basically would like the label of the leaf and the height of the enclosing branch. A dendrogram example

I want to classify bipolar neurons in human cochleas and have data of the following structure: Vol_Nuc Vol_Soma 1 186.23 731.96 2 204.58 4370.96 3 539.98 7344.86 4 477.71 6939.28 5 421.22 5588.53 6 276.61 1017.05 7 392.28 6392.32 8 424.43 6190.13 9 256.41 3850.51 10 249.17 3118.14 11 276.97 3037.29 12 295.30 3703.76 13 314.43 5265.97 14 301.15 5781.73 I

Hi all I am trying to perform the follwing: fit<-pvclust(wq, method.hclust="ward", method.dist="euclidean") but get a strange error message that I just cant figure out. Has anyone come across this? Any help would be most appricieated Error in hclust(distance, method = method.hclust) : NA/NaN/Inf in foreign function call (arg 11) In addition: Warning message: NAs

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

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

I am trying to learn how to format Ascii data files for scan or read into R. Precisely for a quickie project, I found some code (at end of this email) to do exactly what I need: To cluster and graph a dendrogram from package (stats). I am stuck on how to format a text file to run the script. I looked at the dataset USArrests (which would be replaced by my data and labels) using UltraEdit. That

Dear Experts, I am using the below script to generate the heat map of gene expression data. I am using Hierarchical Clustering (hclust) for clustering. Now I want to compare different clustering parameters such as *K-means* clustering, Model Based Clustering, I have two queries: 1. How to incorporate different clustering method in the same code? 2. Is this possible to implement pvclust in the

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

Hi all, I think I have some problems to use correctly the function dendrapply. Let suppose dend is a dendrogram object. I would likde to know the cardinal number of leaves depending of each node of the tree dend. It is right that the command attr(dend,"members") gives the total number of leaves, and attr(dend[[1]],"members") gives the number of leaves for the first left

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