search for: dendogram

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 cluster, and which first level clusters make a second level cluster and so on. Is there a way in R to g...

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) :...

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]]

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( rep("s", 50), rep("c", 50), rep("v", 50)) ir.hclust <- hclust( dist(ir), "average" ) # Hierar...

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 Europ...

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) <- cou...

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!!!

...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 message in context: http://www.nabble.com/heatmap.2-dendogram-algorithm-tp17874789p17874789.html Sent from the R help mailing list archive at Nabble.com.

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) <- cou...

...ean") gclus <- hclust(genedist, method="average") heatmap(matrix[,],Rowv=as.dendrogram(gclus),Colv=as.dendrogram(sclus), col=rbg) So far so good. But what if I want to look at a group of genes that appear to have the same expression pattern in the heatmap? How do I zoom in on a dendogram in a heatmap to look at which genes that are forming the interesting clusters? I would really appreciate if someone could give me a pointer. Best regards. / Johan ******************************************************************************************* Johan Lindberg Royal Institute of Tec...

Hi, I have trouble with the heatmap function (package stats). The row labels are wrongly ordered and don't correspond to the Rowv dendrogram. I know there is a bug with the heatmap fonction. Emmanuel Paradis (http://tolstoy.newcastle.edu.au/R/e2/help/07/05/16227.html )suggested a modification to fix it but in my case the row labels are still wrongly ordered. Heatmaps with 2 phylograms have

...ight=15, width=15, res=100, pointsize=9) library(gplots) library(RColorBrewer) data <- read.table(inputfile) matrix <- as.matrix(data) cp <- colorRampPalette(c("red","yellow","darkgreen"),space="Lab", bias=1.5) heatmap.2(matrix, Colv=1:ncol(matrix), dendogram="row", hclustfun=function(m) hclust(m,method="complete"),col=cp(25),scale="none",trace="none",keysize=1,margins=c(5,12), cexCol=1, cexRow=1) q() dev.off() The alternative that i tried to avoid the reordering was heatmap.2(matrix, Rowv=NULL, Colv=NULL, col=...

...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)) Generating the matrix didn't seem to be a problem. I would appreciate any thoughts and ideas. I have tried using heatmap in bioconductor. However, I want to substitute the dendograms with axes, but when I suppressed the dendogram, I can't successfully add any axis. If anyone knows heatmap() well and would like to help via this function, it would work also. Cheers!Karen Liu [[alternative HTML version deleted]]

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 given by fastgreedy.community in all cases and that the heat map will represent the same clustering. Tell me if my apprehension is incorrect. Otherwise please let me k...

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 anybody have a code for calculating a similarity matrix using the Nei-Li index. My data has either prese...

...o write some resampling routines and sensitivity tests for tree objects. Perhaps this question should go to the r-devel list instead.... Yours, Walton Green > Date: Tue, 06 Jan 2004 12:49:59 +0100 > From: Johan Lindberg <johanl at kiev.biotech.kth.se> > Subject: RE: [R] Analyzing dendograms?? > To: <r-help at stat.math.ethz.ch> > Message-ID: <5.2.0.9.0.20040106122638.00badeb8 at kiev.biotech.kth.se> > Content-Type: text/plain; charset="iso-8859-1"; format=flowed > ...dendograms/heatmaps/hclust in R in a proper way I ask myself, is > there a way...

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

...t to apply the cluster algorithm using single linkage procedure. The metric is the euclidean metric. In order to do this, I do: aux=agnes(xMatrix, diss = inherits(xMatrix,"dist"),metric="euclidean",method="single") Next, I do plot(aux) because I want to view the dendogram. My question is about the graph of the dendogram. What means the number "height" that appears on the left hand of it? My assumption was it was the distance between clusters but I was wrong because the distance matrices between the clusters are the following: Join clusters {3} and {5} (d...

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 R I recently asked for a cluster analysis Using * cluster.results <- hclust(iris.dist, method="complete") * but nothing happened i.e the previous scatterplot matrix still showed up whereas I was expecting a dendogram. Could it be that because I had used cutree before on the scatter plots that it somehow mucked it up. I tried detach then attach and commenced making the data matrix again and followed the procedures through. Not sure what I've done wrong here, can anyone help me brett stansfield