similar to: heatmap -- invisible list?

Hi all, I've got a set of gene expression data, and I'm plotting several heatmaps for subsets of the whole set. I'd like the heatmaps to have the same color distribution, so that comparisons may be made (roughly) across heatmaps; this would require that the color distribution and distance functions be based on the entire dataset, rather than on individual subsets. Does

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

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

I've been using R for a while under Mac OS X, which thanks to the R on OS X developers, is probably the best platform for learning R. I recently built a Linux box with a Pentium D processor, and am running an AMD64 port of Ubuntu with the SMP kernel. After setting up the basics on the box, I thought I'd install R as well. I've had a very hard time finding good documentation

I've been using R for a while under Mac OS X, which thanks to the R on OS X developers, is probably the best platform for learning R. I recently built a Linux box with a Pentium D processor, and am running an AMD64 port of Ubuntu with the SMP kernel. After setting up the basics on the box, I thought I'd install R as well. I've had a very hard time finding good documentation

Hi all, I'm trying to build R 2.1.1 on Ubuntu 5.04 i686-SMP. Configure goes well with: ./configure --with-BLAS --with-readline=no but once I run 'make', I get the following error: In file included from devX11.c:64: devX11.h:57:74: X11/Intrinsic.h: No such file or directory Any ideas? Thanks in advance, Jake

---------- Forwarded Message ---------- Subject: Re: [R] conditional coloring of image labels Date: Friday 11 November 2005 1:04 pm From: jim holtman <jholtman at gmail.com> To: Jake Michaelson <jjmichael at cc.usu.edu> Use 'mtext': genes=cbind(ABC1=c(3,4,4,5,6,3), ABC2=c(4,3,4,7,7,8), ABC3=c(8,7,8,6,3,2)) ###plot the image image(1:nrow(genes), 1:ncol(genes), genes, axes =

Hi all, I am interested in plotting a heatmap of a set of genes. I would like the text labels of these genes to be colored red rather than black if they meet certain statistical criteria (using an if statement). I'm not sure how to change individual color labels without changing them all. Can anyone provide some insight on how to do this? Thanks in advance, Jake

Does anyone know how to extract residuals in lmer? Here's the error I get: > crop.lme=lmer(response~variety*irrigation*pesticide+(1|rep)+(1|rep: pesticide)+(1|rep:pesticide:irrigation), crop.data) > qqnorm(crop.lme) Error in qqnorm.default(crop.lme) : y is empty or has only NAs > resid(crop.lme) NULL Thanks! --Jake

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.

I did a very quick search of the archive and couldn't find a readily available answer to this one: I'd like to convert, for example: c("a", "b", "a", "b") to c(1, -1, 1, -1) In the case of the first vector, it may be any length, but will always only have two unique values. It must always be replaced by corresponding values of 1 and -1. Any

I want to plot a heatmap without reordering the columns. This works fine in "heatmap": > heatmap(meanX[selected,], col=cm.colors(256), Colv=NA) But in "heatmap.2" I get: > heatmap.2(meanX[selected,], col=cm.colors(256), Colv=NA) Error in if (!is.logical(Colv) || Colv) ddc <- reorder(ddc, Colv) : missing value where TRUE/FALSE needed (Note that instructions for

Hi All, I've worked on some code to take a heatmap with 1000 row entries, and split this up into 20 pages, each with 50 rows from the original heatmap. I want to preserve the row order such that all 20 pages, if put together, would comprise the original heatmap. Here's what I've done: ##make the initial heatmap, with all 1000 rows and write it to an object 'heatAll'

Hi All, I'm taking an Experimental Design course this semester, and have spent many long hours trying to coax the professor's SAS examples into something that will work in R (I'd prefer that the things I learn not be tied to a license). It's been a long semester in that regard. One thing that has really frustrated me is that lme has an extremely counterintuitive way for

I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and heatmap.2 gave me completely different outputs. Here are the codes: ------------ > dim(as.matrix(data.dcpm)) [1] 15462??? 18 > > heatmap(as.matrix(data.dcpm), col=topo.colors(100)) > heatmap.2(as.matrix(data.dcpm), col=topo.colors(100), key=TRUE,

Hi all, I would like to be able to call a custom function automatically before plot.new() is called (more specifically, before a new plot is created on the current graphics device). Recently I've been poking around in the help files of some of the low(er) level plotting functions, and I seem to remember something saying that you could somehow add a setting to call a function immediately

Hi, I have a question about the heatmap dendrogram in R. I loaded my data matrix in command heatmap(), and it gave me a heatmap accordingly, and the rows (genes) also were clustered accordingly. But now I don't want the genes clustered in that way, I have a new order of these genes, and want the rows of the heatmap are drawed as the order I give. Could anybody help me on that? Thank you!

Hi, I'm kinda new of the R world. I need to use the heatmap or heatmap.2 function to plot correlation values. 2 questions: - how can I specify a color palette? (would like to have a transition from blue(-1) to white(0) to red(1)) - how can I use heatmap.2 imposing a specific order (like hclust.order)? I mean, I don't want heatmap.2 to re-cluster/re-order my data but just to plot them

Hi, I was trying to use par(mfrow) to put 4 heatmaps on a single page. However, I get one plot per page and not one page with 4 plots. What should I modify? Test code is given below: test = matrix(rnorm(60), 20, 3) pdf(file='test.pdf',width=10,height=8) par(mfrow=c(2,2)) heatmap(test) heatmap(test) heatmap(test) heatmap(test) dev.off() thanks! [[alternative HTML version deleted]]

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