similar to: heatmap.3

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

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),

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 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

I am using heatmap with the arguments below. The title size stays the same no matter what I set cex.main to. Is this expected? Can I adjust the title size in heatmap? Also, the position of the main title is at the very upper edge of the output and if I use a "\n" to stack the title the upper line is out of bounds and doesn't show up. I am outputting to pdf. Any help? Thanks,

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, Does anyone know of a fairly easy way to "stretch" a heatmap vertically? I've got 42 arrays and would like to be able to see as many significant genes as possible (right now I can only get 50 genes with it still being readable). In some comparisons there are several hundred significant genes. I've fiddled with the "asp" argument, but that doesn't

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 <-

Dear list members, I have been using R to create a heatmap where my data has continous variables from 0 to 100. When I create the heatmap, although the branches are correct, they do not order themselves so that the row with the most zeros is at one end and the row with the most 100s is at the other, which is what I would like them to do, so as to create a colour gradient down the graphic. I have

Dear R-Helpers, I have a short question related to heatmap.2 function. I wanted to change the dimension of each cell in the heatmap drawn by this function. here is a reproducible example from the help page library(gplots) data(mtcars) x <- as.matrix(mtcars) rc <- rainbow(nrow(x), start=0, end=.3) cc <- rainbow(ncol(x), start=0, end=.3) hv <- heatmap.2(x, col=cm.colors(255),

Hi Allen and list, See the code below.? I've tried it on R2.13 and R2.8.0 using either heatmap.plus 1.3 or the latest.? All gave the same results.? The problem is in the last line: when I tried to plot two different color bars, the one corresponding to "cm.colors(10)" is not correct (it starts with one black and one red.? Not sure where they're from?) Any ideas? Thanks!

Dear R contributors, Considering the following sample C code, that illustrates two possible uses of a Cholesky decomp for inverting a matrix, equally valid at least in theory: SEXP test() { int d = 2; int info = 0; double mat[4] = {2.5, 0.4, 0.4, 1.7}; double id[4] = {1.0, 0.0, 0.0, 1.0}; double lmat[3]; F77_CALL(dpotrf)("L", &d, mat, &d, &info); lmat[0] = mat[0]; lmat[1]

This isn't the help list for LAPACK, but as far as I can tell, dppsv expects a symmetric matrix input compacted as triangular, not a Choleski decomposed one. So try assigning lmat before the call to dpotrf. -pd > On 20 Dec 2014, at 22:06 , Pierrick Bruneau <pbruneau at gmail.com> wrote: > > Dear R contributors, > > Considering the following sample C code, that

Hi, I wanted to make more than one side color bar. For example, I can make one side color bar (col1) with the following code: ----------------------------------- library(gplots) mat <- matrix(sample(1:100,40),nrow=5) class1 <- c(rep(0,4),rep(1,4)) col1 <- ifelse(class1 == 0,"blue","red") class2 <- c(rep(1,3),rep(2,5)) col2 <- ifelse(class2 ==

Hi everyone, I am fairly new to R, and I am aware that others have had this problem before, but I have failed to solve the problem from previous replies I found in the archives. As this is such a standard procedure in psychological science, there must be an elegant solution to this...I think. I would much appreciate a solution that even I could understand... ;-) Now, I want to calculate a

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 there, I have two questions about heatmap.2 in gplot. My input is a simple square matrix with numeric values between 75 and 100 (it is a similarity matrix based on bacterial DNA sequences). 1. I can sort my input matrix into categories with rowsidecolors (in this case, very conveniently by bacterial taxa). I do a clustering and reordering of my matrix by Rowv=TRUE (and

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

Full_Name: Kevin R. Coombes Version: 2.1.0 OS: Windows XP Submission from: (NULL) (143.111.224.169) When revC = TRUE and RowSideColors is set to a list of colors in heatmap, then the image and dendrogram are inverted, but the row-side color map does not change. The following script illustrates the problem. ############## set.seed(1023) # generate columns of two different types d1 <-

There is a problem with a user mapping a network drive. Sometimes he can map it, sometimes he can't. SAMBA: 3.0-alpha18 UNIX: HP-UX 11.0 rsc is a valid account on the machine he's trying to connect to (entry in /etc/passwd, decent permissions on home directory and all parent directories, etc.) The strange thing is sometimes it works, and sometimes it doesn't. If it doesn't