similar to: Coloured label, terminal branch and bars in dendograms

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)

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

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,

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) >

Hello everyone, Does anyone know how to implement the argument "unit" in R's plclust function ? I used to use Splus where this argument exists but it has not been implemented in R's plclust. The reason why I switched from Splus to R is that Ward's method is not implemented for S's hclust whereas it is implemented for R's hclust. What I would need is S's plclust

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)

>>>>> Ross Ihaka writes: > I have got a little side-tracked (from graphics) and am putting > together a little multivariate analysis library. This is just > intended to be a "core" library rather than anything exhaustive. > Mainly it is a matter of putting togther code which already exists at > StatLib. Here is my present list (only some of which is

Hi all, I need to plot a dendrogram, but I built a hclust object. Follow the code lines: >dendObject<-list(merge=merge,height=height,order=order,labels=labels,call="hclust(d=d)",method="complete", dist.method="euclidean") >class(dendObject)<-"hclust" >plclust(dendObject,axes=FALSE) Error in cl[[2]] : subscript out of bounds Anybody can help

Good afternoon, After cuting a hierarchical tree using cutree(), how to check correspondances between classes and branches? This is what we do: srndpchc <- hclust(dist(srndpc$x[1:1000,1:3]),method="ward") #creation of hierarchical tree plclust(srndpchc,hmin=20000) #visualisation srndpchc20000 = cutree(srndpchc,h=20000) #returns 4 classes table(srndpchc20000 ) srndclass20000 =

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)

I want to plot the cluster trees from the results of hclust() on different datasets, but all with the same distance scale corresponding to the dataset with the largest distance range. However, plclust() does not accept ylim values. Does anyone know of a way around this problem? Mike White

I would like to get an hierarchical clustering tree with bootstrap values indicated on the nodes, as in pvclust. The problem is that I have only distance matrix instead of the raw data, required for pvclust. Is there a way to get it? fit1 <- hclust(dist) # an object of class '"dist" plot(fit1) # dendogram without p values library(pvclust) fit2 <- pvclust(raw.data,

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 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 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 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]]

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 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 all, I'm new to R, so needless to say I have a couple questions (which I hope I haven't missed through the documentation). I have several files in lower triangular matrix form. For each of these matrices, I want to perform some form of hierarchical clustering on each matrix and capture the output of the clustering. The first problem I run into is actually loading the matrix file