similar to: hclust in heatmap.2

Hi When I give the command: > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row ",trace="none",col=greenred.colors(79)) The resulting heatmap has re-ordered my columns! This is time-course data, and I don't want my columns re-ordered! Note from the help: Rowv: determines if and how the _row_ dendrogram should be reordered.

Good afternoon, I ran heatmap and hclust on the same matrix x (strictly, I ran heatmap(x), and hclust(dist(t(x))), and realized that the two dendrograms were slightly different, in that the left-right arrangement of one pair of subclusters (columns) was reversed in the two functions (but all individual columns were grouped correctly). Looking through the code for heatmap as a most definite

Hi Sorry to revisit an old problem, I seemed to solve this in 2004, only for it to resurface :-S I am trying to plot a heatmap, and I don't want the columns of my matrix re-ordered. The function doesn't seem to behave as the help would have you believe: a <- matrix(rnorm(100),nr=20) a.d <- dist(a) a.hc <- hclust(a.d) a.de <- as.dendrogram(a.hc) # columns are re-ordered

Using the heatmap.2 function, I am trying to generate a heatmap of a 2 column x 500 row matrix of numeric values. I would like the 1st column of the matrix sorted from the highest to the lowest values - so that the colors reflected in the first column of the heatmap (top to bottom) go from red to green. After sorting the matrix (z), I tried the following command, but the data remains

Hi, Can someone please guide me towards how to produce "heatmap" output from the output of "hclust" run prior to the actual "heatmap" call? I have some rather lengthy clustering going on and tweeking the visual output with "heatmap" recalculating the clustering every time is not feasible. Thanks, Joh

Full_Name: Shane Neph Version: 2.2.1 OS: mac os x Submission from: (NULL) (71.113.43.247) While I found the names of the package authors and maintainer, I was unsuccessful in finding any contact information. The preliminary documentation for heatmap.2 is inconsistent in at least a couple of places when discussing the suppression of one or more dendrograms (and column/row ordering in general).

Hi, I'm trying to build dendrograms to pass to heatmap(). The dendrograms I build plot properly, but when I pass them to heatmap() I get the error message "row dendrogram ordering gave index of wrong length" (see output log below). I looked in the code of heatmap() and saw that the error was due to a NULL return value from order.dendrogram(), which in turn got a NULL return value

Hello, I've been clustering my data using hclust and cutting the resulting tree with cutree. Separately, I visualize the clusterings with heatmap. Is it possible to have the dendrogram on the heatmap reflect the cutree results? That is, instead of having one large dendrogram, it would have 4 or 25 in the example below. Any guidance on if that's possible or not, and what kinds of

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>

Hi, I have a question about the heatmap dendrogram in R. I loaded my data matrix in command heatmap(), and it gave me a heatmap accordingly, and the rows (genes) also were clustered accordingly. But now I don't want the genes clustered in that way, I have a new order of these genes, and want the rows of the heatmap are drawed as the order I give. Could anybody help me on that? Thank you!

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, I am a beginner for R. I had use gplots to generate a heatmap as following: >heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE, trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering dendrogram and I can export a very nice graph. But I don not know how

Hi all, By default, the heatmap function gives an image with a dendrogram added to the left side and to the top. Is it possible to only add the dendrogram to the left side and let the order of the columns unchanged ? I tried heatmap(mat, col=rbg,Rowv=res.hclust$order,Colv=1:dim(mat)[[2]]). In this case, the order of the columns are unchanged but a dendrogram is added to the top. How can I

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

Esteemed R-users, heatmap.2() is yielding an inappropriate key based on my colors and break-points. In the reproducible example below, the key is inappropriate (to me) because- 1. 'Orange' is simply not represented in the key, despite its prescence in the heatmap. 2. The proportions of the key are clearly out, ie., my largest bin, (0.1 - 0.2) is half the range, but this bin (colored

Under Details, the documentation says "[if Rowv or Colv] is 'NULL', _no reordering_ will be done for the corresponding side." In fact, as explained elsewhere in the documentation, 'NA' is required, not 'NULL'. An anonymous expert suggested that I should attach an svn diff file to this report, so I will. JD -------------- next part -------------- Index:

Hello! I have data containing a large number of probabilities (about 60) of nonzero coefficients to predict 10 different independent variables (in 10 different BMA models). i've arranged these probabilities in a matrix like so: (IV1) (IV2) (IV3) ... p(b0) p(b0) p(b0) p(b1) p(b1) p(b1) p(b2) p(b2) p(b2) ... where p(b1) for independent variable 1 is p(b1 !=

I would like to draw horizontal or vertical lines on a heatmap to highlight the clusters at some specified cut depth of the dendrogram. As a hacked example, the following code would work if I could set the coordinates of the top and bottom of the false color image correctly (ymin and ymax), but the correct values seem to depend on the output device and its size. I realize that heatmaps use a 2x2

I would like to organize my data as follows: I have a table that contains various data, and the numbers represent a level of similarity between these data, eg RF00013 has 100% similarity with the data RF00014. I would leave my table as a heatmap where darker colors represent higher similarity, and the lighter colors represent less level of similarity. I'm using version 2.11 of R. these

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",