search for: dend

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....

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 viewed piecemeal. My problem is this: when I f...

>>>>> 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 ... see below. > I say this is a bug because (I believe), we would like a dendrogram t...

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 le...

...sn'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 delimited text files that contain chromatogram data that I am trying to display adjacent to a dendrogram. Since I look at multiple files I import them as file1, file2, file3, etc. To display them in the order that comes from the dendrogram I want to use order.dendrogram, which gives me a vector of numbers that is the order which I want the chomatograms to be displayed. Here's the...

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,fram...

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 ca...

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...

...;identify", do_identify, 0, 11, 6, PP_FUNCALL}, {"strheight", do_strheight, 0, 11, 3, PP_FUNCALL}, {"strwidth", do_strwidth, 0, 11, 3, PP_FUNCALL}, ! {"contour", do_contour, 0, 11, 6, PP_FUNCALL}, {"image", do_image, 0, 11, 5, PP_FUNCALL}, {"dend", do_dend, 0, 111, 6, PP_FUNCALL}, {"dend.window", do_dendwindow, 0, 111, 6, PP_FUNCALL}, --- 644,650 ---- {"identify", do_identify, 0, 11, 6, PP_FUNCALL}, {"strheight", do_strheight, 0, 11, 3, PP_FUNCALL}, {"strwidth", do_strwidth, 0, 11, 3, PP_...

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 to export the column clusteri...

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 &a...

...g=fxs_ks group=0 channel => 3 context=inside faxdetect=incoming immediate=no signalling=fxo_ks group=1 channel => 4 What should we do in order to make it work ok? we really need to put this working, i've heard that asterisk does not work very well with fax, but at least it should try to dend it, not to get frozen :S Thanks in advance for all your help! Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.digium.com/pipermail/asterisk-users/attachments/20100409/ec63bd44/attachment.htm

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 dend...

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 send...

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 base code? Unquestio...

...from 'irisSAS' data? D = matrix(0, n, n) nam = c('Set', 'Ver', 'Vir') rownames(D) = nam colnames(D) = nam k = 0 for (i in 1:n) { for (j in 1:i) { k = k+1 D[i,j] = Mah[k] D[j,i] = Mah[k] } } D=sqrt(D) #D2 -> D library(mclust) dendroS = hclust(as.dist(D), method='single') dendroC = hclust(as.dist(D), method='complete') win.graph(w = 3.5, h = 6) split.screen(c(2, 1)) screen(1) plot(dendroS, main='Single', sub='', xlab='', ylab='', col='blue') screen(2) plot(dendroC, mai...

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 by referring to the DEND_IND variable using its symbol, like it's done in the lapply() implementation. > The problem i...

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 what I?m used to. I had written a slightly improved version of dendrapply for one of my research projects, and my advisor encouraged me to submit it to the R project. It took m...