similar to: The question is on Symmetry model for square table.

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 <-

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 would need some help to fix polybench/symm: void kernel_symm(int ni, int nj, DATA_TYPE alpha, DATA_TYPE beta, DATA_TYPE POLYBENCH_2D(C,NI,NJ,ni,nj), DATA_TYPE POLYBENCH_2D(A,NJ,NJ,nj,nj), DATA_TYPE POLYBENCH_2D(B,NI,NJ,ni,nj)) { int i, j, k; DATA_TYPE acc; /* C := alpha*A*B + beta*C, A is symetric */ for (i = 0; i < _PB_NI; i++) for (j = 0; j < _PB_NJ; j++) {

On Fri, Oct 14, 2016 at 6:10 PM, Hal Finkel <hfinkel at anl.gov> wrote: >> polybench/linear-algebra/kernels/symm, FP_ABSTOLERANCE=1e1 >> polybench/linear-algebra/solvers/gramschmidt, FP_ABSTOLERANCE=1e0 >> What should be a good relative tolerance to set for these two tests? > > What's the minimum relative tolerance that you need for them to pass? Setting

On Fri, Oct 14, 2016 at 10:50 AM, Hal Finkel <hfinkel at anl.gov> wrote: > ----- Original Message ----- >> From: "Renato Golin" <renato.golin at linaro.org> >> To: "Sebastian Pop" <sebpop.llvm at gmail.com> >> Cc: "Hal Finkel" <hfinkel at anl.gov>, "Sebastian Paul Pop" <s.pop at samsung.com>,

Hi, I'm a PhD student and I want to use the function 'daisy' from the package 'cluster' to compute dissimilarities. My variables are of mixed types so I use the argument 'stand' in daisy to define the type of my variables. I have the following error message : Warning message: binary variable(s) 13, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,

On Mon, Oct 10, 2016 at 5:02 PM, Hal Finkel <hfinkel at anl.gov> wrote: > ----- Original Message ----- >> From: "Sebastian Pop" <sebpop.llvm at gmail.com> >> To: "Hal Finkel" <hfinkel at anl.gov> >> Cc: "Sebastian Paul Pop" <s.pop at samsung.com>, "llvm-dev" <llvm-dev at lists.llvm.org>, "Matthias

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",

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>

On Wed, Oct 12, 2016 at 10:28 AM, Hal Finkel <hfinkel at anl.gov> wrote: > ----- Original Message ----- >> From: "Renato Golin" <renato.golin at linaro.org> >> To: "Hal Finkel" <hfinkel at anl.gov> >> Cc: "Sebastian Paul Pop" <s.pop at samsung.com>, "llvm-dev" <llvm-dev at lists.llvm.org>, "Matthias

On Wed, Oct 12, 2016 at 10:53 AM, Hal Finkel <hfinkel at anl.gov> wrote: > I don't think that Clang/LLVM uses it by default on x86_64. If you're using -Ofast, however, that would explain it. I recommend looking at -O3 vs -O0 and make sure those are the same. -Ofast enables -ffast-math, which can legitimately cause differences. > The following tests pass at "-O3" and

On Tue, Oct 11, 2016 at 10:39 PM, Sebastian Pop <sebpop.llvm at gmail.com> wrote: > On Tue, Oct 11, 2016 at 10:20 PM, Hal Finkel <hfinkel at anl.gov> wrote: >> ----- Original Message ----- >>> From: "Renato Golin" <renato.golin at linaro.org> >>> To: "Sebastian Pop" <sebpop.llvm at gmail.com> >>> Cc: "Hal

Hi, I already have a dissimilarity matrix and I am submitting the results to the elbow.obj method to get an optimal number of clusters. Am I reading the below output correctly that I should have 17 clusters? code: top150 <- sampleset[1:150,] {cluster1 <- daisy(top150 , metric = c("gower") , stand = TRUE , type = list(symm

Hi everyone, I do a lot of work with large variance matrices, and I like to use "crossprod" for speed and to keep everything symmetric, i.e. I often compute "crossprod(Q %*% t(A))" for "A %*% Sigma %*% t(A)", where "Sigma" decomposes as "t(Q) %*% Q". I notice in the code that "crossprod", current definition > crossprod function (x,

Hi, I run into following error when using heatmap() for data matrix "xx". Any help is appreciated? "xx" contains many "NA"s. > hv <- heatmap(data.matrix(xx)) Error in hclustfun(distfun(if (symm) x else t(x))) : NA/NaN/Inf in foreign function call (arg 11) Thanks a lot. Yuhong

Dear List, I'm trying to generate a simple heatmap that has each row and column separated by a black line. However, for some reason this only happens for the first and last color. The middle color in my colorpanel() command has an addition horizontal and vertical line that I would like to get rid off. Any suggestions? #my code below my.matrix <- cbind(func.1 =

I'm trying to display the probability space of a function and wanted to see specifically where the maximum posterior probability is. data=read.table("PosteriorData",header=F) mat=as.matrix(data) heatmap.2(mat/max(mat,na.rm=T),dendrogram=c("none"),trace=c("none"), Rowv=F,Colv=F,labRow=3*c(10:-10),labCol=3*c(-10:10),symm=T,col=rainbow(100)) As the

----- Original Message ----- > From: "Renato Golin" <renato.golin at linaro.org> > To: "Sebastian Pop" <sebpop.llvm at gmail.com> > Cc: "Hal Finkel" <hfinkel at anl.gov>, "Sebastian Paul Pop" <s.pop at samsung.com>, "llvm-dev" <llvm-dev at lists.llvm.org>, > "Matthias Braun" <matze at

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)) :

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