similar to: error "evaluation nested too deeply" {was "Heatmap"}

I'm diverting this to the more appropriate mailing list, R-help, since heatmap() is standard R function. >>>>> "Johan" == Johan Lindberg <johanl at kiev.biotech.kth.se> >>>>> on Fri, 02 Jan 2004 10:04:14 +0100 writes: Johan> I am trying to plot a matrix of m-values in a heatmap Johan> with "average linkage". The rows

Hi, I get following error when trying to plot a heatmap on a very large matrix (808 x5000). heatmap(ctab) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? Call to heatmap function is not contained within any other function or so. Upon searching the R mailing list, I found that someone had the same problem and the suggested solution was to set an option using

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:

I recently started using R (Version 1.3.0 on a Dell machine). After using R for about a week, I started receiving the error message shown below. I can't even run simple commands that I know should work. Is this a bug or did I just mess something up? I've uninstalled and reinstalled R but continue to receive the same errors. The errors are shown below: R : Copyright 2001, The R

hello all i searched the archives and couldn't get a solution to the following question. i have the following function: F=function(z,v) { if (v==-.5) return(1) else return(2*v/z + 1/Recall(z,v-1)) } and while testing whether it works (ie F(z,v) is approx = besselK(z,1+v)/besselK(z,V). the recursion formula allows one to calculate besselK(z,1+v)/besselK(z,V) for large values of z )

Hi, I am processing tick data and my code has stopped working as I have increased the size of data being processed. Now I am receiving error for basic tasks in RConsole: > a = c(1:1000) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? My R code worked fine with 50 stocks and 500,000 rows per stock, but when I increased this to 50 stocks and 5,000,000 rows per

I get the error Error : evaluation nested too deeply: infinite recursion / options(expressions=)? during a 'R CMD check ...' on one of my packages. The reason seems to be that this package is mutually dependent on another one (i.e. the DESCRIPTION files of package A lists package B under "Depends" and vice versa). this might be bad design (having bits in both packages needed

hello R-users, I'm trying to port from S+4 a library called S2HTML. generic function HTMLExport, when called for a lm object, uses HTMLExport.lm which itself calls HTMLExport.list to export the summary. My problem is that HTMLExport.list may itself call HTMLExport (and so HTMLExport.list) for components of the lists that are lists themselves (like "terms" component of an lm object).

Hi guys, I have a code in R and it was work well but when I decrease the epsilon value (indicated in the code) , then I am getting this error Error: evaluation nested too deeply: infinite recursion / options(expressions=)? any help please y = 6.8; w = 7.4; z = 5.7; muy = 7; muw = 7; muz = 6; sigmay = 0.8; sigmaz = 0.76; sigmaw = 0.3; betayx = 0.03; betayz = 0.3; betayw = 0.67 s =

Hi all, Why I am getting, Error: evaluation nested too deeply: infinite recursion / options(expressions=)? Thanks in advance! func <- Vectorize(function(x, a, sad, trunc=0, ...) { result <- function(x) { f1 <- function(n) { dcom <- paste("d", deparse(substitute(sad)), sep="") dots <- c(as.name("n"), list(...)) f <-

hello all i searched the archives and couldn't get a solution to the following question. i have the following function: F=function(z,v) { if (v==-.5) return(1) else return(2*v/z + 1/Recall(z,v-1)) } and while testing whether it works (ie F(z,v) is approx = besselK(z,1+v)/besselK(z,V). the recursion formula allows one to calculate besselK(z,1+v)/besselK(z,V) for large values of z )

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

Dear all, I generated a heatmap with the heatmap() function with the default "complete" linkage method, but when I add the argument Rowv=as.dendrogram(hclust(dist(matrix), method="complete")), The dendrogram generated is different from the dendrogram produced by heatmap() with default settings. Could someone kindly point out where my mistakes are? P.S. When I did

Hi, I am trying to create a heatmap with some specific requirements. Specifically, I need to be able to center the color-scale around 0, and I need to truncate the data so that a few extreme values do not cause the rest of the heatmap to appear black (on a red/green scale). After reading through and experimenting with heatmap, heatmap.2, heatmap_plus, and heatmap_2, I believe heatmap.2 will

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 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 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

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).

Dear R users, I'm trying to create images of 2 symmetrical matrices using heatmap.2 of the 'gplots' library. Both matrices have the same row and column names For the first matrix I'm using the default clustering and column denrogram options: heatmap.2(Matrix1, symm=T, breaks=20, col=rich.colors(19), main="matrix1", density.info="histogram",

Hello, I would like to display a heatmap with dendrograms and allow the user to click on either dendrogram to choose a sub-dendrogram. The function heatmap() uses layout() and image() and the plot method of dendrogram to plot the heatmap and dendrograms, but if locator() is then called and the user clicks, the coordinates returned from locator() are with respect to the last thing plotted (e.g.,