similar to: how to resize heatmap without rescaling?

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

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

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, 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 I am having some problems getting my heatmap to be the right size! Let me explain. I am experienced at getting an hclust or a dendrogram object to be the right size. For example, I have a dataset which has 4000 rows, which I clustered using hclust and I wanted to plot it as a horizontal dendrogram. So I used jpeg(), set the image height to be 4000 and plotted the dendrogram and got the

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 list, I am using heatmap.2(x) to draw a heatmap. Ideally, I want to the matrix x clustered only by columns and keep the original order of rows unchanged. Is there a way to do that in heatmap.2()? Thanks a lot! Any suggestions will be appreciated! Best, Allen [[alternative HTML version deleted]]

Hello all, I am using the heatmap.2 function in the gplots package. I want to supress the reordering of the columns of the data matrix i pass to the function. I used the statement, heatmap.2(z,Colv=FALSE,dendrogram="row",col=redgreen(75)) where z, is the matrix of data. The output i want should have the rows reordered along with the dendrogram and the columns should be in the original

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

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

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 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.

Hi, Is there a way I can draw an abline on a heatmap? I try the abline function, but don't get the line. My sample code is: mat <- matrix(sample(1:100,40),nrow=5) heatmap(mat,col=greenred(75),trace="none", dendrogram = "column",labCol = NULL) abline(h=5,v=4) thanks! [[alternative HTML version deleted]]

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

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!

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 <-

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

Hi, I want to generate a heatmap for my data (in a matrix). However, the data has some missing values (represented as blank). I get the following errors (with the blanks and with blanks replaced by NA and including the option rm.na = TURE): > filename = "input_heatmap.txt" > g <- as.matrix(filedata) > fg <- rainbow(nrow(g), start=0, end=.3) > gg <-

Using the heatmap function in mva, it seems to be hard to use different colors in the edges leading to different groups of objects, as commonly done in many heatmaps in the microarray graphics. Any suggestions? Thanks. max