similar to: A "bug" in plot.dendrogram - can't plot lty with character color

>>>>> Tal Galili <tal.galili at gmail.com> >>>>> on Mon, 18 May 2015 23:01:44 +0300 writes: > The problem: > =========== > Once a dendrogram has a branch with both a line type AND a color (which is > a character color), the plot.dendrogram function will not plot and return > an error. If the dendrogram has been messed up

Core developers, I couldn't find any simple way to send a vector of colors to apply to each terminal in plot.dendrogram() or plot.hclust()---I asked R-help about it a few weeks ago and didn't get any response---so I hacked that functionality into the plot.dendrgram code (see below for hacked function plus examples).... Is there any chance this functionality could be added to the

Dear Martin, You are right. When implementing the dendextend::set function, I failed to notice that edgePar should accept a list instead of a vector. So all I did was to discover a bug in my own code. I am both sorry for taking your time due to my own mistake, and also grateful for your help (I will resolve this bug before submitting the next release to CRAN). I am sure that I would have had

Dear all, for my diploma thesis I have to import huge XML-Files into R for statistical processing - huge means a size about 33 MB. I'm using the XML-Package version 1.9 As far as reading the complete file into R via xmlTreeParse doesn't work or is too slow, I'm trying to use xmlEventParse but I got completely stuck. I have many different type of nodes + <configuration>

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 everyone, My apologies if this isn?t the right place to submit this?I?m new to the R-devel community and still figuring out what is where. If people want to skip my writeup and just look at the code, I?ve made a repository for it here: https://github.com/ahl27/new_dendrapply/tree/master. I?m not quite sure how to integrate it into a fork of R-devel; the package structure is different from

Dear useRs, I am working on a project involving the clustering of a large dataset. I need to extract specific sub-clusters from the parent dendrogram for further analysis. The data is too large for the use of convenient tools such as identify.clust (it selects the specific group of interest on a graph), so alternatively I have saved the plot as a large image file so that it can be printed or

Hello all, I've run into what I bet is a silly problem; however, I've been trying to get around it now for a couple weeks and every time I think I have the answer it still doesn't work. So I apologize in advance if this is painfully obvious, but I've run out of ideas and would really appreciate any input. My situation is this, I'm importing a number of tab

Following "Introduction to dendextend" from Tal Galili, I applied this code on iris data: ## library(dendextend) library(dendextendRcpp) library(ggplot2) dend2 <- iris[1:30,-5] %>% dist %>% hclust %>% as.dendrogram %>% set("branches_k_color", k=3) %>% set("branches_lwd", rep(1,4)) %>% set("branches_lty", rep(1,6)) %>%

hi all, i'm trying to plot a dendrogram with labeled leaves >rownames(f)<-v.names >v<-rowMeans(f, na.rm=T) >clust<-hclust(dist(v)) >dend<-as.dendrogram(clust,hang=0.05) >clust2<-cut(dend, h=0.5) >class(clust2$low[[1]]) >[1] "dendrogram" then >plot(clust2$low[[1]],horiz=TRUE,frame=F,type = "tr")) but my leaf labels do not fit

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

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Hello all, A question/suggestion: I was wondering if there is a chance of changing stats::cutree to be S3 and use cutree.hclust? For example: cutree <- function(tree, k = NULL, h = NULL,...) { UseMethod("cutree") } cutree.hclust <- stats::cutree # This will obviously need the actual content of stats::cutree This would be nicer for people like me to add new methods to

Hello my friends... We are having some problems with the fax in our asterisk server... We have: Asterisk 1.4.21.2 Zaptel Version: 1.4.11 libpri version: 1.4.5 Digium Card TDM 410P This digium card has 3 FXO ports and 1 FXS port where we have a fax machine connected! The problem is that we can receive fax very good, but we can't make any outbound fax call, in fact, our asterisk get freezed

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

Hi all, I think I have some problems to use correctly the function dendrapply. Let suppose dend is a dendrogram object. I would likde to know the cardinal number of leaves depending of each node of the tree dend. It is right that the command attr(dend,"members") gives the total number of leaves, and attr(dend[[1]],"members") gives the number of leaves for the first left

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 found it useful to have contour be able to do line widths ... hope that the guts haven't changed an enormous amount in the current development version ... the patches are relatively trivial, mostly going by analogy with lty and col (although in my ignorance it took me a while to figure out what UNPROTECT(2) was and why it should be changed to UNPROTECT(3) ... hope this is useful. Ben

Hello there, I spent all day yesterday trying to get a small data set from Splus into R, no luck! Both, Splus and R, are run on a 64-bit RedHat Linux machine, the versions of the softwares are 64-bit and are as what follows: Splus: TIBCO Software Inc. Confidential Information Copyright (c) 1988-2008 TIBCO Software Inc. ALL RIGHTS RESERVED. TIBCO Spotfire S+ Version 8.1.1 for Linux 2.6.9-34.EL,

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 <-