similar to: rotating an hclust tree with negative hights

Hello, The following code does'nt work for me. The last command reports an error. I have created a consensus tree using the consensus comand from phylo but cannot manipulate the phylo object afterwards to create a dendogram , by transforming the phylo object into a hclust object and then into a dendogram ?? Thanks for any help library(ade4) library(cluster) library(stats) library(ape)

The R function hclust is used to do cluster analysis, but based on R help I see no way to print the actual fusion distances (that is, the vertical distances for each connected branch pairs seen in the cluster dendrogram). Any ideas? I'd like to use them test for significant differences from the mean fusion distance (i.e. The Best Cut Test). To perform a cluster analysis I'm using: x

Hello, I have a question. I creat a PDF file with four rows and two cols. Is it possible to: -create a plot regions with different hights (example: rows 1 & 2-4) -ro center an image in the whole width (example: rows 4) Thank's a lot. Felix example: -------- Title -------------------------------- |Text |Text | |Text |Text | --------------------------------- | | | | | |

Hi Vahid, I suggest you use a more recent version. The latest version is 3.0. Ciao, Duncan. On 20/02/12 09:27, vahid eslami wrote: > > 0 down vote favorite > <http://stackoverflow.com/questions/9354312/llvm-2-8-dswp-core-dump-linux#> > share [g+] share [fb] share [tw] > > i new in llvm.i just compile google code and got this error. " Stack dump: 0. > Program

0 down vote favorite [http://stackoverflow.com/questions/9354312/llvm-2-8-dswp-core-dump-linux#] share [g+] share [fb] share [tw] i new in llvm.i just compile google code and got this error. " Stack dump: 0. Program arguments: opt -load /home/vahid/mywork/llvm-2.8/Release/lib/DSWP.so -dswp obj.o -o out.o 1. Running pass 'Function Pass Manager'

I am using R for hierarchical clustering of a number of documents. I have a distance matrix on which I have applied hclust method. When I plot the result of hclust method, I can see the dendogram plotted. What I need now is the dendogram stored as a tree in a data structure. My goal is to automatically label all internal nodes. For that, I need to know, which leaf nodes make a first level

Hello. I have the following distance matrix between 8 points: [1,] 0.000000 3.162278 7.280110 8.544004 7.071068 9.899495 6.403124 8.062258 [2,] 3.162278 0.000000 5.000000 6.403124 4.472136 8.944272 6.082763 8.062258 [3,] 7.280110 5.000000 0.000000 1.414214 1.000000 5.000000 4.242641 5.830952 [4,] 8.544004 6.403124 1.414214 0.000000 2.236068 4.123106 4.472136 5.656854 [5,] 7.071068 4.472136

Hi everyone, I am using the fastgreedy.community function to get the $merges matrix and the $modularity vector. This serves my purpose of testing modularity of my graph. But I am "greedy" to plot the heat map and dendrrogram based on the $merges dendogram matrix. I know that heatplot does the graphics part but I am not sure if the dendogram generated by the heatplot will match the one

Hello everyone! I have two questions regarding cluster analysis with the package 'cluster' : 1. I have a dissimilarity matrix in csv format, and I would like to use it to generate a dendogram using 'hclust'. How do I make that matrix compatible with the function? I think it has to be similar to the objects generated by the 'dist' function. Any ideas? 2. Does

Dear R-help, I have performed a hierarchical clustering on some data that I have and would like to know some nice ways of visualizing it. I have 2 related questions: i) How to color the labels AND the terminal branch of a dendogram? This is my inelegant way of just getting the colored labels. data(iris) # Formatting data into required format ir <- iris[ ,-5] ir.class <- c(

Hi, I''ve recently installed xen-3.2.1 on my AMD Sempron(tm) machine. It runs gentoo 2.6.21 as dom0 and cpu frequency scaling works in dom0. But inside a domU, cpu frequency scaling is not working. By checking the boot log in domU I found that domU is unable to load the powernow driver: "powernow-k8: BIOS error - no PSB or ACPI _PSS objects" I wonder if it is possible to have

Hi,   I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.    I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using. args <- commandArgs(); inputfile <- args[2] imgfile   <- args[3] bitmap(imgfile, height=15, width=15, res=100,

Hi, Does Xen provide support for CPU frequency scaling? If there exists such support, from which version they support it? Otherwise what problems do exist in support frequency scaling in Xen? Thanks, Vahid _______________________________________________ Xen-devel mailing list Xen-devel@lists.xensource.com http://lists.xensource.com/xen-devel

Hi, I have Samba 3.0.21b running on Solaris 10 with ADS authentication. I get the following in log.winbindd when I do "getent passwd" but wbinfo -u lists all the users. Does anyone know why and how to fix it? Thanks, Vahid. [2006/02/04 13:37:02, 3] nsswitch/winbindd_ads.c:query_user_list(234) ads query_user_list gave 9926 entries [2006/02/04 13:37:04, 3]

Dear All, I am trying to find a way to plot a dendogram in reverse, that is, if the terminal leaves are labelled 1-10 bottom to top (or left to right), I would like to be able to plot it in a way such that if would display 10-1 bottom to top or left to right. Any idea how to achieve this? Thanks in advance, r. Dr. Rafael Najmanovich European Bioinformatics Institute Wellcome Trust

I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames) >

Dear all, I need to make dendogram from read count in a csv file across 34 samples including biological replicate. Please share R code or package to do this. Do I also need to normalized read count before using read data? Thanks [[alternative HTML version deleted]]

The data "one" is a vector of 553 observations agglone<-agnes(one, metric = "manhattan", stand = TRUE) plot(agglone,which.plots=2, nmax=150) My problem is in the dendogram, I can not see the nodes because it is too crowded. I have attached the diagram. Any help is more than welcome. Thank you a lot!!!

Hello does anyone know what algorithm is used to produce the hierarchical clustering in the gplots package using the function heatmap.2? I think it may be the complete linkage clustering algorithm, but I can't find a source that seems reliable. Thank you and sorry if I posted this in the wrong place. If I have, please let me know and I will move it to the appropriate list. -- View this

Dear All, I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames)