similar to: meaning of order-vector in object of class hclust

Hello, The heatmap function conveniently has a "reorder.dendrogram" function so that clusters follow a certain logic. It seems that the hclust function doesn't have such feature. I can use the "reorder" function on the dendrogram obtained from hclust, but this does not modify the hclust object itself. I understand that the answer should be within the "heatmap"

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 all, I manually created an hclust object. Now I am looking to reorder the leafs so they won't intersect with each other, and would be happy for advises on how to do that. Here is an example code: #------------------------------------- a <- list() # initialize empty object # define merging pattern: # negative numbers are leaves, # positive are merged clusters (defined by row

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

Hi! I am newbee to R and I am facing the problem in plotting the dedrogram with lot of objects. The lines and labels are overlapped very badly, and writing the graphic to postscript and zooming there is not helping either. I tried cut.dendrogram method, but getting the error that it doesn't exist even though I get the man pages for it. I would not find any solution in web as well, and I

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 group members, I am looking for a function that assess the stability of cluster. The result of hclust function is an hclust object which can be plot as a dendrogram. However to have confidence in the tree topology usualy bootstap is applied. I understand that I can apply bootstarp on the original data and then run hclust(dist() ) as much as I resampled but how to comapre the topologies the I

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

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

Hi, I have an hclust object say hcl with heights starting from a negative and ending to a positive value. I would like to rotate the plot(hcl) 90 degrees clockwise. It is suggested to use plot(as.dendogram(hcl), horiz=T) but I encountered two problems: 1) a dendrogram object does not accept negative heights 2) horiz=T rotates the tree 90 degrees unclockwise any ideas? thanks, Vahid PARTOVI

I am making heatmaps for a dataset (~ 300*600 matrix) with the following R script (I am not familiar with R and this is the first time I am using it). library("gplots") library("Cairo") mydata <- read.csv(file="data.csv", header=TRUE, sep=",") rownames(mydata)=mydata$Name mydata <- mydata[,2:297] mydatamatrix <- data.matrix(mydata) mydatascale

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

I have a data set with 6 variables and 251 cases. The people who supplied me with this data set believe that it falls naturally into three groups, and have given me a rule for determining group number from these 6 variables. If I do scaled.stuff <- scale(stuff, TRUE, c(...the design ranges...)) stuff.dist <- dist(scaled.stuff) stuff.hc <- hclust(stuff.dist)

This worked for me with your example: source("dumpdata.R") storage.mode(x.hc$merge) <- "integer" plot(x.hc) (R-1.4.1 compiled from source on WinNT4.) Andy > -----Original Message----- > From: Hugh Chipman [mailto:hachipma at icarus.math.uwaterloo.ca] > Sent: Wednesday, February 20, 2002 5:32 PM > To: andy_liaw at merck.com > Cc: r-help at stat.math.ethz.ch

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 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

I've found that while cutree() and rect.hclust() make the same classes for a given height in the dendrogram, the actual labeling of the classes is different. For example, both produce the same 4 classes but class 1 according to cutree() is class 4 according to rect.hclust(). Would it be possible that future versions provide the same labeling? rect.hclust() is useful to display the classes

Hi All Not sure if this a bioconductor question or general R mailing list so apologies if this has gone to the wrong one................. When plotting dendrograms created by hclust you can "identify" clusters by clicking on the graphics and returning a list of what is contained in each cluster. However I'd like to be able to "zoom in" on specific clusters and plot

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

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 +++