similar to: reordering materix presentation in heatmap.2 in the 'gplots' library

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

Thanks Tom. heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen, breaks=seq(-1,1,by=0.01), symm=TRUE, trace="none", dendrogram="none") that did the trick :) Begin forwarded message: From: "Leja, Thomas" Date: 29 March 2011 03:47:59 GMT+01:00 To: "Benton, Paul" Subject: Re: [R] comparing heatmaps Yep, you have to specify the range for colours. I usually

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, On R 2.10.1 for Windows, when I do the following to duplicate the structure of a large numeric matrix called matrix1: matrix2 <- matrix(0,nrow=nrow(matrix1),ncol=ncol(matrix1)) and then rownames(matrix2) <- rownames(matrix1) I get a "cannot allocate vector of size xxMb" error but if I instead do: rnames <- list() rnames <- rownames(matrix1) matrix2 <-

Hello, I have two matrices as shown below: Matrix 1 ID AB1 BC1 CD1 ... name1 1,1 2,1 0,2 ... name2 2,0 1,2 1,2 ... name3 0,2 1,1 2,0 ... name4 2,0 0,2 0,2 ... Matrix 2 ID AB2 BC2 CD2 ... name1 1,1

Dear R team, The following piece of code (to use the lsa package) works fine on my mac os x, but when I run the same code on Windows XP, it doesn't work any more. ### code: library("lsa") matrix1 = textmatrix("C:\\Documents and Settings\\tine stalmans.TINE. 000\\LSA\\cuentos\\", stemming=TRUE, language="spanish", minWordLength=2, minDocFreq=1,

Hi, I have two table matrix, and I would like to compare the different between two matrix. For example: Matrix 1: A B C A 0 1 0 B 0 0 1 C 0 0 0 Matrix 2: A B C A 0 1 0 B 0 0 0 C 0 0 0 Each column which have value 1, should also return value 1. As in this case/example, the result should appear like this (as below). The result of this differentiation should also be in matrix

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, just during these vacation days, I'm trying to approach with multicore package and I have some troubles with foreach. What I'm trying to do is to extract a data in coordinate (ii,jj) from a matrix2, only if the data in the same coordinate in matrix1 is ==1. Make this with a nested "for" take a lot of time because I have thousand of values. ex. Binary_hex = NULL

Full_Name: Manuel L?pez-Ib??ez Version: R version 2.6.2 (2008-02-08) OS: linux-gnu Submission from: (NULL) (164.15.10.156) This is only relevant for CPU intensive child processes. Otherwise, the problem is not obvious. Therefore, we need a CPU intensive program like this one: /************************************/ /*** Compile with: gcc -o timer-test -O0 timer-test.c -lm */ #include

Hi, I'm new to programming, new to R and even new to mailing lists so please be patient with me. I need to manage many matrices generated by an R program. These matrices have different dimensions and I'd like to group them somehow. The best way would be to have a big matrix (let's call it database) where every element database[x,y] consists of a list of matrices that all have the

Hi R-users I have a series of matrices and I would like to bind them together by column using a loop (i.e. not writing cbind(matrix1, matrix2,matrix3....)). The reason is because in my real data set I have a very large number of matrices. Example: matrix1 <- matrix (1:12,4,3) matrix2 <- matrix (13:24,4,3) matrix3 <- matrix (25:36,4,3) matrix4 <- matrix (37:48,4,3)

I have two matrix with same dimensions. I want to do t.test using each column from 2 different matrix. Row n Column names in both matrix are same. e.g. Matrix1 id VC1 VC2 VC3 R 1 2 3 R1 4 5 6 R3 7 8 9 Matrix2 id VC1 VC2 VC3 R 10 11 12 R1 13 14 15 R3 16 17 18 want to do t.test using each column (with same name ) using Matrix1 and Matrix2 for eg

Hi, thank you for taking the time and reading my question. My question is twofold: 1. I have several matrices with variables and one matrix with water levels. I want to predict the water level with the data in the other matrices. Basically, * mod<-lm(matrix1 ~ matrix2+matrix3)* ( What looks like a minus is meant to be the wiggly minus.) Of course I could dissemble the matrices and paste

Hello, I have got two matrices with different length. The matrices have 3 columuns. The first two are coordinates. The third is a measurement. Now I want to get a subtraction between every single value of the third column (between matrix1 and matrix2), but only if the two first coordinates in matrix1 and matrix2 are the same. I tried "FUN=?" in aggregate and ave, but I don't know

I have two matrix with same dimensions. I want to do t.test using each column from 2 different matrix. Column names in both matrix are same. e.g. Matrix1 id VC1 VC2 VC3 R 1 2 3 R1 4 5 6 R3 7 8 9 Matrix2 id VC1 VC2 VC3 R 10 11 12 R1 13 14 15 R3 16 17 18 want to do t.test for eg t.test(Matrix1$VC1, Matrix2$VC1)$p.value What is the best way to do it. I have dataset with

I have a question related to matrix(). The code below randomly generates 3 Poisson numbers into a 3 by 1 matrix: > matrix1 <- matrix(rpois(3,lambda=2),nrow=3,ncol=1) And I use list() to see what they are: [,1] [1,] 3 [2,] 1 [3,] 4 , which is what I had intended. I then I want to randomly generate y Normal numbers into a 3 by 8 matrix. y in this case would be 3, 1, and 4; so

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 =

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).

Let's say that I have a bunch of matrices. They look like this (pardon using fruit for examples, my actual data tables are far too enormous): Matrix1 Apples Oranges Pears A 5 6 7 B 5 3 4 C 8 9 10 D 11 13 14 E 15 3 8 F 1 4 5