similar to: Colors in a dendrogram

Hello, i'm a research student working on everyday sounds classification. i need to draw a dendrogram to show how the classification is done, but while i never used R before, i guess that a help from someone would be great :) does any one of you did something like that before? Thank you -- Ayoub

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

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'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

Hi! I just discovered that cutree() and cut.dendrogram() do not assign the same cluster numberings when called on the same tree. More specifically, cutree() assigns cluster numbers by order of appearance in the data, while cut.dendrogram() sorts clusters by height (see example below). I guess this is for historical reasons? I'm hit by this difference when I want to get a vector of cluster

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 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

Hi all, I'm having a problem where by I'm trying to use the NeatMap draw.dendrogram function as it is more versatile in placement/direction of dendrograms, instead of the limited plot function. Using plot I can get my dendrograms to display the species name for each leaf of the tree. But I cannot figure out how to make this happen using draw.dendrogram.. genetic<-

Dear R users, I have created data for hierarchical agglomerative cluster analysis which consist of the merging pairs and the agglomeration heights, e.g. something like my.merge <- matrix(c(-1,-2,-3,1), ncol=2, byrow=TRUE) my.height <- c(0.5, 1) I'd like to plot a corresponding dendrogram but I don't know how to convert my data to achieve this. Is it possible to create a

Dear all, I am using the hclust method in R. I am building nice dendrograms with it. Actually for my further analysis I want to get the number of bifurcations (bif) for each object (labels) in the dendrogram. That has to be calculated by the colums merge, height and order. http://www.nabble.com/file/p16142989/Sc2Mown_Pred.txt Sc2Mown_Pred.txt Sc2Mpred<-

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, How to plot the dendrogram or tree for kmeans, like we do for hclust ? [[alternative HTML version deleted]]

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 +++

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

Dear R-users, I need some help concerning the plotting of dendrograms for hierarchical agglomerative clustering. The agglomeration niveau of each step should be displayed at the branches of the dendrogram. For this I need the x/y coordinates of the branch-agglomerations of the dendrogram. The y-values are known (the heights of the agglomeration), but how can I get the x-values? > mydata

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

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

?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!

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

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: