search for: hclust

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 "dump...

...xample programme which demonstrates this effect. I uploaded a PDF showing the results Here is the code which produces the PDF file: ------------------------------------------------------------------------------------- s <- matrix(runif(1600,0,1000), nrow=20) a.res1 <- pvclust(t(s), method.hclust="complete", method.dist="euclidian", nboot=500) a.res2 <- pvclust(t(s), method.hclust="complete", method.dist="maximum", nboot=500) a.res3 <- pvclust(t(s), method.hclust="complete", method.dist="canberra", nboot=500) a.res4 <- pvc...

...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 > Subject: Re: [R] plot.hclust: strange behaviour with "manufactured" > > > Andy: > > That's a great idea. And it's certainly part of the problem. I > verified this by changing the type of the "merge" element of a valid > hclust object to be double. As you suggest, it doesn&...

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 s...

Having some problems with using hclust.identify on my data, I revert to trying it out on the example in the help manual. My result is still the same (as with my own data): data(iris) hci <- hclust(dist(iris[,1:4])) plot(hci) testx<-identify.hclust(hci) Error in rect.hclust(x, k = k, x = x$x, cluster = cluster[, k - 1], border...

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 eleme...

...if (!is.null(rownames(rawdata))) attr(rawdata.dist, "Labels") <- rownames(rawdata) } else rawdata.dist <- dist(rawdata, method = method.distance) if (!method.transform == "identity") rawdata <- trans(rawdata, method.transform) hclust.results <- hclust(rawdata.dist, method = method.cluster) pMatrix <- cbind(hclust.results$merge, matrix(data = NA, nrow = nrow(hclust.results$merge), ncol = 1)) simprof.results <- simprof.body(rawdata = rawdata, num.expected = num.expected, num.simulated = num.simula...

I could not figure out what was the default when I ran hclust() without specifying the method. For example: I just have a code like: hclust(dist(data)) Any input would be appreciated:) [[alternative HTML version deleted]]

Hello, I would like to cut a hclust tree into several groups at a specific similarity. I assume this can be achieved by specifying the "h" argument with the specified similarity, e.g.: clust<-hclust(dist,"average") cut<-cutree(clust,h=0.65) Now, I would like to draw rectangles around the branches of the de...

Hi, this is rather a (presumed) bug report than a question because I can solve my personal statistical problem by working with hclust instead of agnes. I have done a complete linkage clustering on a dist object dm with 30 objects with agnes (R 1.8.0 on RedHat) and I want to obtain the partition that results from a cut at height=0.4. I run > cl1a <- agnes(dm, method="complete") > cutree(cl1a,h=0.4) [1] 1...

Hi, this is rather a (presumed) bug report than a question because I can solve my personal statistical problem by working with hclust instead of agnes. I have done a complete linkage clustering on a dist object dm with 30 objects with agnes (R 1.8.0 on RedHat) and I want to obtain the partition that results from a cut at height=0.4. I run > cl1a <- agnes(dm, method="complete") > cutree(cl1a,h=0.4) [1] 1...

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). Lo...

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:...

Hello, I am using the hclust function to cluster some data. I have two separate files with the same data. The only difference is the order of the data in the file. For some reason, when I run the two files through the hclust function, I get two completely different results. Does anyone know why this is happening? Does the...

...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 red, where all the other labels are black. Now, the only tree I can use the "user-click" with is an hclust object, with the identify.hclust() function. As far as I know, neither the dendrogram objects or the output of heatmap is cut-able in this way. So I have the sub-tree and plot drawing set up on user-click using an hclust object and identify.hclust - good :) Therefore I am working with hclust ob...

Dear R users, I have noted a difference in the merge distances given by hclust using centroid method. For the following data: x<-c(1009.9,1012.5,1011.1,1011.8,1009.3,1010.6) and using Euclidean distance, hclust using centroid method gives the following results: > x.dist<-dist(x) > x.aah<-hclust(x.dist,method="centroid") > x.aah$merge [,1]...

I am doing a cluster analysis with hclust. I want to get hclust to output the Hotelling's T squared statistic for each cluster so I can evaluate is data points should be in a cluster or not. My research to answer this question has been unsuccessful. Does anyone know how to get hclust to output the Hotelling's T squared statistic...

Hello! I have the following problem. I would like to plot the hclust object "hcd" (bellow, at the end of the mail) with ticks at seq(0.05,0.25,by=0.05). I tried using the code plot(hcd) and plot(hcd,axes=FALSE) axis(2,seq(0.05,0.25,by=0.05)) In both cases, the resoult is the same, ticks at 0.05 and 0.25 are not printed. I tried changing the ylim argumet...

Dear group, I am currently struggling with the following problem for a while: I want to create a list whose elements consists of lists themselves. More concise: The list elements are HCLUST objects. However, when I try to append the HCLUST objects to my list via: cluster_list <- append(cluster_list, HCLUSTobject) the HCLUST object is appended - but not as an object but as its components. So cluster_list[[1]] will not return the HCLUST object, but the first element of the first cl...

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 don...