similar to: comparing heatmaps

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

Posting for a friend Begin forwarded message: From: "Geier, Florian" <florian.geier08@imperial.ac.uk<mailto:florian.geier08@imperial.ac.uk>> Subject: Fwd: readBin fails to read large files Date: September 1, 2011 4:10:53 PM GMT+01:00 To: Begin forwarded message: Date: 1 September 2011 16:01:45 GMT+01:00 Subject: readBin fails to read large files Dear all, I am trying

Hello all, I am using the heatmap.2 function in the gplots package. I want to supress the reordering of the columns of the data matrix i pass to the function. I used the statement, heatmap.2(z,Colv=FALSE,dendrogram="row",col=redgreen(75)) where z, is the matrix of data. The output i want should have the rows reordered along with the dendrogram and the columns should be in the original

Hello all R-er, I'm trying to run a resampling method on some data. The current method I have takes 2+ days or a lot of memory . I was wondering if anyone has a better suggestion. Currently I take a matrix and get the correlation matrix from it. This will be called rho.A. Each element in this will be tested against the distribution from the resampled correlation B matrix. Some example

Hello, I have a large (919 X 919), hierarchically clustered heatmap that I would like to read the labels off of. I have tried saving the figure in pdf format and enlarging it until I can see the labels, but if I make the labels small enough to read (so that they don't overlap) using cexRow and cexCol, they do not appear in the pdf. The limit seems to be anything below cexRow or Col = 0.06.

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

Hi, I'm trying to save heatmaps as PDFs. However, the PDF version of the heatmaps (Heatmap_CAFvsTNF_run2.pdf) is blurred when compared to its counterpart, which was saved manually by using the software "Grab" (Heatmap_CAFvsTNF_run2.tiff). -----R code-------- sample_output <- "stroma_run2" filename <-

Hi , I am trying to plot a heatmap with a correlation matrix and trying to highlight significant correlations . i am using my matrix d874n has 78 columns ex2<-corAndPvalue(data.matrix(d874n),use = "pairwise.complete.obs") ##creating a matrix of true false using p values sig<-ex2$p<0.05 nx=78 ny=78 makeRects <- function(tfMat,border){ cAbove =

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 searched for a solution but I failed to find an answer. I am hoping you may be able to help me. I have a data set where I have observations for a number of units (n =~40) over a period of time (t =~100) and I have a variable (Z) that codes a categorical variable for each observation. I want to produce a 2D plot where time is on the x-axis and units are on the y-axis. Then each block

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",

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 generated a heatmap in R using the following commands: > mydata <- read.csv(file="Data.csv", header=TRUE, sep=",") > mydata <- mydata[rowSums(mydata[,-1]^2) >0, ] > rownames(mydata)=mydata$Name > mydata <- mydata[,2:253] > mydatamatrix <- data.matrix(mydata) > mydatascale <- t(scale(t(mydatamatrix))) > hr <-

I generated a heatmap in R using the following commands: > mydata <- read.csv(file="Data.csv", header=TRUE, sep=",") > mydata <- mydata[rowSums(mydata[,-1]^2) >0, ] > rownames(mydata)=mydata$Name > mydata <- mydata[,2:253] > mydatamatrix <- data.matrix(mydata) > mydatascale <- t(scale(t(mydatamatrix))) > hr <-

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

Hi, I have a question about heatmap. I have a data with row as microRNA and two columns are two cell expression values for these microRNA. So, like: cell1 cell2 miRNA1 1.5 3.4 miRNA2 1.3 2.4 ................... miRNA50 5 2.1 miRNA51 7.3 0.5 I want to see some miRNA are high in cell1 and low in cell2 but others are low in cell1 and high in cell2. I

Dear R users, I am trying to print heatmaps in a loop (with a pause). Idea is to visualize changing correlations over time and for testing I wrote this simple (reproducible) code below. My problem is that levelplot() does not produce any output when I run the code (though heatmap does). Ideally I would like to use levelplot() as it produces a neat index on the side indicating the color and the

Hi all, I tried testing with Rspec for first time, following a tutorial. "rspec spec/" works fine but when I try ''autotest'' it gives me the error message below. I also made a gist about it: https://gist.github.com/779265 It seems like a redgreen or ZenTest error. I''m using Ubuntu10, Rails3, Ruby 1.9 and RVM. Any help is appriciated, thanks in advance, gezope

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

Hi Sorry to revisit an old problem, I seemed to solve this in 2004, only for it to resurface :-S I am trying to plot a heatmap, and I don't want the columns of my matrix re-ordered. The function doesn't seem to behave as the help would have you believe: a <- matrix(rnorm(100),nr=20) a.d <- dist(a) a.hc <- hclust(a.d) a.de <- as.dendrogram(a.hc) # columns are re-ordered