similar to: hclust and heatmap - slightly different dendrograms?

I have written a wrapper for heatmap.2 called heatmap.w.row.and.col.clust which auto-generates breaks using breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20, digits = 2) #(stddev in this case = 2.5) This has always worked well in the past but now I am getting an error that non-finite breaks are being generated. Drilling down, it seems that my wrapper is generating finite

Hi, I run into following error when using heatmap() for data matrix "xx". Any help is appreciated? "xx" contains many "NA"s. > hv <- heatmap(data.matrix(xx)) Error in hclustfun(distfun(if (symm) x else t(x))) : NA/NaN/Inf in foreign function call (arg 11) Thanks a lot. Yuhong

Hello, I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something. When calling the function in symmetric mode, the ColSideColors are plotted correctly, but RowSideColors appear in reverse order. This code (modified from the example on the help page) demonstrates the problem: cU <-

Dear R wizards, Hopeful someone can help me with what I believe is a pretty simple task. I pretty new to R so some (much) of the obvious escapes me. How do I get a distance matrix into heatmap? What do I tell distfun if what I'm trying to map is already an ordered distance matrix? I tried >heatmap(x, distfun=as.dist(x)) where x is the distance matrix but R gave me an error. Thanks in

Hi netters, I have a matrix X of the size (1000,100). The values are from -3 to +3. When I tried heatmap(X, distfun=function(c),dist(c,method="bin"),hclustfun=function(m),hclust(m,method="average")) I got the error message: Error: evaluation nested too deeply: infinite recursion / options(expressions=)? However, if I used default parameters for distfunction:

Hi, Could you please help? Heatmap doesn't work with: > heatmap(as.matrix(SPIV2),na.rm = T) Error in hclustfun(distfun(x)) : NA/NaN/Inf in foreign function call (arg 11) There are no 0 data rows or column Thanks a lot Regards --------------------------------------- David

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

Hi, I am using heatmap.2 of gplots to make heatmaps of my the attached file. I am giving my code for the same .. library(gplots) x=read.table("1.txt", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("both"), scale = c("row"), na.rm=TRUE, trace="none",

Hi, I''m using heatmap.2 to cluster my data, using the centroid method for clustering and the maximum method for calculating the distance matrix: library("gplots") library("RColorBrewer") test <- matrix(c(0.96, 0.07, 0.97, 0.98, 0.50, 0.28, 0.29, 0.77, 0.08, 0.96, 0.51, 0.51, 0.14, 0.19, 0.41, 0.51), ncol=4, byrow=TRUE)

Hi, I am having troubles with heatmap(). I have a matrix containing pairwise distance values and I want to plot this matrix with heatmap. I wonder now what distfun is for. Is a distance matrix computed from my initial matrix again and then plotted? cheers, andreas

Full_Name: Zivan Karaman Version: 2.7.2 OS: Windows XP Submission from: (NULL) (195.6.68.214) I'm puzzled by the readRegistry function. Shouldn't the "hive" argument be something like c("HLM", "HCR", "HCU", "HU", "HCC", "HPD") rather than c("HLM", "HCR", "HCU", "HU",

Dear Dr. Liaw Andy: I have a few more questions about your heatmap function. actually heatmap is what I am looking for. heatmap(x, Rowv, Colv, distfun = dist, hclustfun = hclust, add.expr, scale=c("row", "column", "none"), na.rm = TRUE, ...) my data is a XNEW, > dim(XNEW) [1] 554 335 554 genes, 335 samples. now I want to use 1-CORR as a distance

heatmap.2 defaults to dist for calculating the distance matrix and hclust for clustering. Does anyone now how I can set dist to use the euclidean method and hclust to use the centroid method? I provided a compilable sample code bellow. I tried: distfun = dist(method = "euclidean"), but that doesn't work. Any ideas? library("gplots") library("RColorBrewer") test

Hi all, I am a novice user of the heatmap.2 function in the Bioconductor gplots package. I am trying to create a heatmap diagram from a hierarchical clustering result based on the complete linkage and the pearson correlations as the distance metrics. After reading the help page for heatmap.2, it seems that it calls the distfun and hclustfun with the default settings. Is that the same as doing

Hi all, The function heatmap uses the functions dist and hclust with default parameters. How to change these parameters? For example, i want to use the ward criterion for hierarchical clustering with binary distance. Best regards, Olivier.

Hi Kevin, >>>>> "krc" == krc <krc at odin.mdacc.tmc.edu> >>>>> on Mon, 27 Jun 2005 21:55:37 +0200 (CEST) writes: krc> Full_Name: Kevin R. Coombes krc> Version: 2.1.0 krc> OS: Windows XP krc> Submission from: (NULL) (143.111.224.169) krc> When revC = TRUE and RowSideColors is set to a list of krc>

Dear Experts, I am using the below script to generate the heat map of gene expression data. I am using Hierarchical Clustering (hclust) for clustering. Now I want to compare different clustering parameters such as *K-means* clustering, Model Based Clustering, I have two queries: 1. How to incorporate different clustering method in the same code? 2. Is this possible to implement pvclust in the

Hi, I am drawing a heat map using gplots of R package. The file (new4) is having values 0 and 1 only. library(gplots) library(marray) x=read.table("new4", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("black","red"))(256), #col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("row"), scale =

Hi, Can anyone tell me how to set Z-score according to my own requirement as the below code is taking as per the file entries. Any help would be appreciable. library(gplots) x=read.table("final.txt", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("green","white","red"))(256), #col=greenred(75), Rowv=TRUE, Colv=FALSE, distfun = dist,

Dear all, I've been trying to find how to compare tow different heatmaps but I'm having trouble getting the colors bar to be the same. I'm doing something like the following: library(gplots) dat<-cor(matrix(rnorm(100, m=10), nrow=10)) mat<-cor(matrix(rnorm(100), nrow=10)) dev.new() heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen(75), symm=TRUE, trace="none",