search for: dendrograms

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...

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 yo...

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

...t groups the rows (vertical axis) by the abundance pattern (as above), I would like to force it to order and display a dendrogram indicating their evolutionary relatedness. I am using the excellent ape package (http://cran.r-project.org/src/contrib/Descriptions/ape.html) to import the evolutionary dendrograms. I have already manipulated the dendrogram to be ultrameric, with branches all the same length, to prevent an error, although I would prefer not to have to do so: library(ape) mytree <- read.tree(file = "ultra.newick", text = NULL, tree.names = NULL, skip = 0, comment.char = "#&...

I'm clustering rather large data sets and would like to cut the dendrograms to get a better view of specific components. I calculate the dissimilarity matrix using daisy() because I have a mixture of variable types: factors, ordered factors and numerical variables. If I want one dendrogram, I use agnes() for the agglomerative nesting and pltree() to draw the dendrogram....

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...

Hi When I give the command: > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row ",trace="none",col=greenred.colors(79)) The resulting heatmap has re-ordered my columns! This is time-course data, and I don't want my columns re-ordered! Note from the help: Rowv: determines if and how the _row_ dendrogram should be reordered.

...usters that I need to analyze I have no way to reference that specific component of the dendrogram in order to extract it: smallDend <- dend[[i]][[j]][[k]] where i,j,k refer to levels of the dendrogram (it's "address") I would like to print the "address" of the smaller dendrograms on the edge similar to this: addr <- function(n) { if(!is.leaf(n)) { attr(n, "edgetext") <- paste("height of",(attr(n,"height")) } n } labeledDends <- dendrapply(dend, addr) Where "i,j,k" is printed instead of "height...

...there is an obvious explanation for the following problem. My goal is to perform WGCNA on a dataset of 19776 genes, so I opted to follow the block-wise network construction (Section 2c) in the WGCNA R Tutorial by Peter Langfelder and Steve Horvath. I ended up with 10 blocks and am able to plot the dendrograms and module colors for each block, but I am having trouble grouping all of the blocks together for a single dendrogram/module color figure. On page 4 of section 2c in the WGCNA tutorial, the single-block network construction workspace is loaded and it contains a variable called 'geneTree'. g...

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

...om "hclust" objects via as.dendrogram(<hc-obj>) or also "twins" objects produced from package cluster's agnes() or diana() via as.dendrogram(as.hclust( <twins-obj> ) ) help(dendrogram) also mentions "[[" (and shows examples) and cut() for cutting dendrograms and shows how you can depict dendrograms into its parts. michael> With intelligent use of hclust -> cutree -> subsetting -> hclust michael> (in that order) you will be able to drill down michael> into your dendrogram and create sub-trees - until michael> you ge...

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...

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, hres <- hclust(smatr,method="single") hresd<-as.dendrogram(hres) as.dendrogram(hres) `dendrogram' with 2 branches and 380 members total, at height 2514.513 plot(hresd,leaflab="none") #<-error here. #the plotted dendrogram is incomplete. The x axis is not drawn. #The interested reader can download the save(hresd,file="hres.rda") #from the

...Submission from: (NULL) (71.113.43.247) While I found the names of the package authors and maintainer, I was unsuccessful in finding any contact information. The preliminary documentation for heatmap.2 is inconsistent in at least a couple of places when discussing the suppression of one or more dendrograms (and column/row ordering in general). In the Details section, in regards to the Rowv and Colv parameters, "If either is NULL, no reordering will be done for the corresponding side." The default value for these parameters is NULL. With NULL, the dendrograms are computed (and hence reorde...

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

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, 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

...) vs. stats:::plot.dendrogram(ddr,horiz=T,axes=F,yaxs="i",leaflab="none") What variable / line of code corresponds to this additional margin space? I would like to modify the code to remove the extra space and have that margin equal to that when horiz=T, for plotting multiple dendrograms for one images on the same device. Thanks in advance, best. [[alternative HTML version deleted]]

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