similar to: How do I get internal nodes of dendograms produced by R?

I have Windows XP Professional Version 2002 and the R-Version 2.1.1. I did cluster analysis with the cluster package and the agnes (method = ?ward?). The results are satisfactory. But the dendrogram of agnes is confused to work with the results. Is there a tool, I can get a clear arrangement of the results for the cluster analysis. For example a matrix with different numbers for each group.

I have used heatmap to visualize my microarray data. I have a matrix of M-values. I do the following. #The distance between the columns. sampdist <- dist(t(matrix[,]), method="euclidean") sclus <- hclust(sampdist, method="average") #The distance between the rows. genedist <- dist(matrix[,], method="euclidean") gclus <- hclust(genedist,

Dear R I recently performed a cluster analysis. It produced the dendogram no problem but unfortunately the font size of the row.names were all cluttered due to their large size So I tried to change the font size using plclust(cluster.results, labels=iris$specie, cex=0.8) and R came back to me saying Error in plclust(cluster.results, labels = iris$specie, cex = 0.8) : unused argument(s)

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,

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 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

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

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 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(

I have a data which contain some NA value in their elements. What I want to do is to **perform clustering without removing rows** where the NA is present. I understand that `gower` distance measure in `daisy` allow such situation. But why my code below doesn't work? __BEGIN__ # plot heat map with dendogram together. library("gplots") library("cluster")

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

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 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

Ladies and Gentlemen, As Johan Lindberg points out, the documentation for handling dendrograms is sparse....Does anyone know who is responsible for or working on development of tree methods and objects? I've written a couple of scripts for my own use to translate between parenthetical (A(B(CD))) or binary A00 B10 C11 D11 tree formats and cluster objects in R, but as an inexperienced

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]]

I want to do hierarchical cluster analysis to compare 10 groups of vectors with five vectors in each group (i.e. I want to make a dendogram showing the clustering of the different groups). I've looked into using dist and hclust, but cannot see how to compare the different groups instead of the individual vectors. I am thankful for any help. Anders

Dear all, I'm trying to use some technic to do a pattern recognition over a large dataset. I really don't have any idea on how to do that using R. Here is a sample of the data: id,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15 1480010,208,69,180,465,465,241,241,69,584,26,75,578,507,75,284 1480183,208,69,352,476,531,495,163,241,69,584,69,584,69,484,69

When I use the image() function for a relatively small matrix it works perfectly, eg.x <- 1:100 > z <- matrix(rnorm(10^4),10^2,10^2) > image(x=x,y=x,z=z,col=rainbow(3))but when I want to plot a larger matrix, it doesn't really work. Most of the times, it just plot a few intermitent points.x <- 1:1000 z <- matrix(rnorm(10^6),10^3,10^3) image(x=x,y=x,z=z,col=rainbow(3))

Hi everybody! Anybody knows how can I get detalied information about clusters after using hclust? The issue is that if I have some items in different clusters, I would like to get the cluster where each item is placed. Taking into account that my data set is too large, it is not useful to have the dendogram or a graphic, and really I need something like a simple table with item label and cluster

Hi, Environment: Samba version: 4.1.11 or above. Windows: Server 2012 R2/Windows 8 Linux: Fedora 21 Scenario: I have accessed the file in Ubuntu as an administrator and opened it but when I'm trying to enumerate the opened files using NetFileEnum() it shows an error that enumerating files is only possible as an administrator. Kindly help. Thanks and regards, Anirvan Roy Choudhury.