similar to: no labels when plotting dendrograms

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

Hello, It seems that the plot function for dendrograms does not draw labels when they are too long. > hc <- hclust(dist(USArrests), "ave") > dend1 <- as.dendrogram(hc) > dend2 <- cut(dend1, h=70) > dd <- dend2$lower[[1]] > plot(dd) # first label is drawn > attr(dd[[1]], "label") <- "aaaaaaaaaaaaaaaaaa" > plot(dd) # first label is

Hi! In the example: hc <- hclust(dist(USArrests), "ave") dend1 <- as.dendrogram(hc) dend2 <- cut(dend1, h=70) Do the branches "Branch 1", "Branch 2", "Branch 2"...in dend2$upper str(dend2$upper) --[dendrogram w/ 2 branches and 4 members at h = 152] |--[dendrogram w/ 2 branches and 2 members at h = 77.6] | |--leaf "Branch 1" (h=

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

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

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 r-list, I am trying to visually seperate the two main clusters of a dendrogram. The idea is to use: 'edgePar=list(lty=3)' for 'dend1[[1]]' and 'edgePar=list(lty=1)' for 'dend1[[2]]' I have not found a way to solve this. Any suggestions? Patrick hc <- hclust(dist(USArrests), "ave") (dend1 <- as.dendrogram(hc)) par(mfrow=c(2,2)) plot(dend1)

Hi All, i've problem to understand how to work with R to generate a hierarchical clustering my data are in a csv and looks like : idcode,count,temp,sal,depth_m,subs 16001,136,4.308,32.828,63.46,47 16001,109,4.31,32.829,63.09,49 16001,107,4.302,32.822,62.54,47 16001,87,4.318,32.834,62.54,48 16002,82,4.312,32.832,63.28,49 16002,77,4.325,32.828,65.65,46 16002,77,4.302,32.821,62.36,47

Hello to all, I'd like to colour the different labels of my dendrogram. How can I do? I guess I could to 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") plot(dend1) labels (USArrests) [[1]] # to know how many cities

I'd like to change the way plot.hclust displays an hclust object. Here's a description of how it's done now, from the R documentation of hclust: In hierarchical cluster displays, a decision is needed at each merge to specify which subtree should go on the left and which on the right. Since, for n observations there are n-1 merges, there are 2^{(n-1)} possible

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 When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a hierarchial cluster analysis, I end up with a vertical tree. What do I need to do to get a horizontal tree? Also, my users are used to seeing trees who's leaves all "end" at the same place (eg. Like in minitab). Is this possible in R? Thanks Mick Michael Watson Head of Informatics Institute for Animal

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 have done a cluster analysis doing: 1-clusNorth <-hclust(dist(Artorious)^2, method="ward") 2-clusNorth$labels <-Artorious$Name ## to show the case names and not numbers 3-dend1 <- as.dendrogram(clusNorth) 4-plot(dend1) My Dendrogram is now showing the names of my cases in the dataframe on the x axis 1 OMNICELL INC COM 2 GETTY IMAGES INC

> I have performed clustering analysis with hclust (Ward's method) on a > database of 800 samples. As you may imagine the full dendrogram is not > really readable. I have obtained groups with cutree. I would like to plot > sub-sections of my big dendrogram to show group 1, group 2 and so on. I don't think R has anything like subtree in Splus, unfortunately. I think what has

Hello all I've been using the hclust and as.dendrogram objects for hierarchical clustering. The problem I have is that my sample set is now so large (circa 500 points) that it isn't possible to view the leaf nodes. I'd like to be able to zoom in on specific areas of the graph by selecting a region with the mouse. I've deduced from trial and error that the xlim and ylim

Dear list, I am trying to plot a radial dendrogram using the ape package, which requires my data to be of class 'phylo'. Currently I have my dendrogram stored as an object of class 'dendrogram' which was produced from an outside bit of C code, but was made into an object of class 'igraph.eigenc' and converted to a dendrogram using 'as.dendrogram()' from the igraph

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

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:

Hi, I'm trying to build dendrograms to pass to heatmap(). The dendrograms I build plot properly, but when I pass them to heatmap() I get the error message "row dendrogram ordering gave index of wrong length" (see output log below). I looked in the code of heatmap() and saw that the error was due to a NULL return value from order.dendrogram(), which in turn got a NULL return value