search for: dends

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. I say this is a bug because (I believe), we would like a dendrogram to be able to use character colors, while also allowing control over line types. This e-mail includes an example, and what I think a solution

..."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". But I have not been able to figure out how to ask each dendrogram its address within the dendrapply function. Can anyone help me with this? Many thanks, Jesse PhD Student in Social Science Syracuse U...

>>>>> 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

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

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

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

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

im using plclust and want the labels to be different colors. i took a look at getS3method("plot","hclust") and saw a call to .Internal. i looked at the help on .Internal and dont know where to go next. any help appreciated! thanks, rafael

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

I can not tell from the docs or from the mailing list what is the state of timezone support in the iCalendar package? If I want to parse an iCalendar file that has non utc dstarts and dends will it convert those times to UTC or otherwise allow me to do that? When I tried to parse an iCalendar input file started off with something like this: BEGIN:VCALENDAR METHOD:REQUEST PRODID:Microsoft CDO for Microsoft Exchange VERSION:2.0 BEGIN:VTIMEZONE TZID:(GMT-05.00) Eastern Time (US &am...

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

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 in plot, however I got a

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

Hello, My name is Rodrigo, I am using R program and I have a trouble. I am trying to do a dendrogram with genetics information. Let me explain... The Similarity Matrix was already did, and with this matrix I want to construct a dendrogram. So, the distance is done. I need to transform this matrix (that I have) in a dendrogram, I woud be very grateful if someone could help me. PS: I am sending

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 R list, I'm trying to calculate Mahalanobis distances for 'Species' of 'iris' data as obtained below: Squared Distance to Species From Species: Setosa Versicolor Virginica Setosa 0 89.86419 179.38471 Versicolor 89.86419 0 17.20107 Virginica 179.38471 17.20107 0 This distances above were obtained with proc

Hello Aidan, Sorry for dropping this for a while. ? Thu, 2 Mar 2023 21:03:59 +0000 "Lakshman, Aidan H" <AHL27 at pitt.edu> ?????: > //after > curnode = eval(lang3(R_Bracket2Symbol, parent->node, DEND_IND), env); lang3() always constructs a new language object. If you do end up using eval(), it may make sense to move lang3() out of the loop and reuse the existing object

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