similar to: Draw a Dendrogram

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

Hello, i'm trying to draw a dendrogram to show the clustering hierarchy. i'm working on 2 classes but each class contains more than 3000 instances. i'm using the hclust function to do that! but i can't read anything from this figure. i would like to color each class with its own color so at least i can extract some information from the clustering. does any one of you did

Dear all, I would like to draw a dendrogram and mark some parts/branches (by using "segments") including their labels. If I draw it without specifying the length of x axix, I am able to do that (as in My dendrogram 1 of the following codes). However, if I want to specify the x axix, I am not able to draw marking line (by using "segments") including labels (as in My dendrogram

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'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 all, i performed a clusteranalysis - which worked so far... i plotted the dendrogram and sooo many branches, a rough sketch would be enough ;) i tried max.levels therefore which worked, but not for the plot... i used the following plot(hcd,nodePar =nP, str(hcd,max.level=1)) the output on the terminal was: --[dendrogram w/ 2 branches and 196 members at h = 2.70] |--[dendrogram w/ 2

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 a beginner for R. I had use gplots to generate a heatmap as following: >heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE, trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering dendrogram and I can export a very nice graph. But I don not know how

Hi all, ok, i know i can cut a dendrogram, which i did. all i get is three objects that a dendrograms itself. for example: myd$upper, myd$lower[[1]], myd$lower[[2]] and so on. of course i can plot them seperately now. but the lower parts still have hundreds of branches. i?ll need a 30 " widescreen to watch the whole picture. what i?d like to is group the lower branches , so that i get a

Hello, Is it possible to remove those extra margins on the "sample" axis from plot.dendrogram: par(oma=c(0,0,0,0),mar=c(0,0,0,0)) ddr<-as.dendrogram(hclust(dist(matrix(sample(1:1000,200),nrow=100)))) stats:::plot.dendrogram(ddr,horiz=F,axes=F,yaxs="i",leaflab="none") vs. stats:::plot.dendrogram(ddr,horiz=T,axes=F,yaxs="i",leaflab="none")

Hi, I am clustering objects using the agnes() function and the UPGMA clustering method (function = "average"). Everything works well, but apparently something is wrong with the dendrogram. For example: x<-c(102,102.1,112.5,113,100.3,108.2,101.1,104,105.5,106.3) y<-c(110,111,110.2,112.1,119.5,122.1,102,112,112.5,115) xy<-cbind(x,y) library(cluster) UPGMA.orig<-agnes(x)

Hi all, Can someone tell me how to justify (right or left) the labels on the branches of a dendrogram tree? I have produced a dendrogram via agnes and plotted it with pltree. The dendrogram terminal branch labels seem to be centre-justified by default and I was hoping to change this to left justification. Thanks, Duncan ***************************************** Dr. Duncan Mackay School of

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:

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 All, I have a cluster object based on a dissimilarity matrix from about 1,100 cases and wish to know whether anyone can think of any tips to display some form of graphical output which would give some sense of the similarity between the cases. A standard form of dendrogram would be fine, but with so many cases the dendrogram on the standard devices (R-2.20 on NT4) is very compact

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

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 <-

Hello, I have been using the "cophenetic" function for objects of class "dendrogram" and I have realised that it gives different results when it is used with objects of class "hclust". For instance, running the first example in the help file of the "cophenetic" function, d1 <- dist(USArrests) hc <- hclust(d1, "ave") d2 <-

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! 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=