similar to: heatmap aspect ratio

Hello again, lately I have been playing a lot with heatmap functions, in particular I complemented heatmap.2 with a nice feature from heatmap.plus, i.e. the possibility of assigning a matrix to ColSideColors so to take into account more annotations. Below is the code I introduced in heatmap.2, everything else is maintained equal to heatmap.2: if (!missing(ColSideColors)) { #if

Hi R users, I'm a quite extensive user of the heatmap() function, and as many others i'm frequently frustrated by its fixed square width / height ratio. Here is a typical example : dev.new() heatmap(matrix(rnorm(1200), nrow=10)) I have a non square matrix to plot with heatmap, as there are many more columns than rows, row labels are larger than necessary but column labels

Dear list, I have a question on moving color keys when side color bars are added to a heatmap. The R code below produces the color key in the upper left corner. Notice I have added side bars to the heatmap, but how could I move the color key below the image? ------ library(gplots) data(mtcars) x <- as.matrix(mtcars) rc <- rainbow(nrow(x), start=0, end=.3) cc <- rainbow(ncol(x),

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 am trying to understand what happen with the heatmap.2 code that it used to work (last used in October 2015). I am able to get a heatmap but my colour key doesn't come up and instead I get an error in all my files the used to work. Does anyone has any idea of what could have changed? or how to fix this. Thanks. # Error in seq.default(min.raw, max.raw, by = min(diff(breaks)/100)) :

Hi all, I've got a set of gene expression data, and I'm plotting several heatmaps for subsets of the whole set. I'd like the heatmaps to have the same color distribution, so that comparisons may be made (roughly) across heatmaps; this would require that the color distribution and distance functions be based on the entire dataset, rather than on individual subsets. Does

Full_Name: Elizabeth Purdom Version: 1.9.1 OS: Windows XP Submission from: (NULL) (171.64.102.199) It would be great if heatmap and/or image had the option of printing a legend bar on it somewhere that would indicate the ranges given by the colors in the heatmap (i.e. a very small image rectangle with the same colors as in the heatmap). Because heatmap is using layout, it seems pretty

Hi all, In heatmap's documentation, it mentions that the output value is actually an invisible list...how would one access this list? Thanks, Jake

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 Sorry if this is in the help :-S I've looked at example(dendrogram) and though it gives some indication of what I want, it doesn't do all. OK, so here is what I want to do: draw a tree, and then have an action, on user-click, to either draw a sub tree or a plot of the data. I also want users to be able to search for a particular label and have it highlighted on the tree, say in

Hello R-Helpers, I have a question about extracting the clusters of genes after we make the heatmap (say ht4) using the heatmap.2 function. Basically, I want to get the clusters which are shown as row dendrogram in the heatmap. I understand that ht4$rowDendrogram is an object of dendrogram and it containes details of all the nodes and branches, but lets say I want to know the number of clusters

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, 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'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

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 am using the function heatmap(stats) to draw a microarray heatmap, columns are samples and rows are gene features. I did a 2D clustering during the heatmap drawing. The features and samples indeed cluster into several blocks both vertically and horizontally. I can get the index of re-ordered rows and columns after the heatmap drawing by typing the the return variable of the heatmap

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, I am interested in plotting a heatmap of a set of genes. I would like the text labels of these genes to be colored red rather than black if they meet certain statistical criteria (using an if statement). I'm not sure how to change individual color labels without changing them all. Can anyone provide some insight on how to do this? Thanks in advance, Jake

Hello! I looked for help through google and the help-files and spend several hours with trial and error, but didn't find a correct way. It's all about lines in a heatmap to separate different data block from each other to underline the significance of the found clusters! The heatmap is build like that: heatmap(X, Rowv=NA, Colv=NA, symm=TRUE, cexRow=0.3, cexCol=0.3) I switched the

I'm working on some heatmaps, and the person I'm working with would prefer a red-black-green color palette (red denoting gene induction and green denoting gene repression). Does such a palette exist already? If not, is there an easy way to create one? Thanks, Jake