similar to: Re : Half of a heatmap

Hi, I noticed recently when installing the GDD package for R under GNU/Linux that it required the gd library (http://libgd.org/) for generating graphics. The resolution of this was to simply install the library on my system, and then GDD successfully installed without any complaints. However, the variant of GNU/Linux that I use is Gentoo, so I filed a bug requesting that a USE flag be set for

Hi, I'm trying to cast() some data, but keep on getting the following error... > norm.all.melted.height <- transform(all.melted.height, + norm.height = value / ave(value, SNP, Pool, FUN = max) + ) Warning messages: 1: In FUN(X[[147L]], ...) : no non-missing arguments to max; returning -Inf 2: In FUN(X[[147L]],

Hi all, I've just started using the Friedrich Leisch's Sweave package to generate LaTeX reports with results of my analyses embedded as required. I've encountered a bit of a problem though in the processing of the resulting *.tex file that is as far as I can tell, down to the fact that my variable names have underscores ('_') in their names. The relevant section of code

Can R handle graphic text ? I mean something like a pop-up message window or a text widget ? Thank you so much. -- Maura E.M

Hello to everyone! I have built CRAN task view for genetics. For now I have not submit it to CRAN yet and it can be accessible from: http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv I have not submitted it to CRAN, since I would like first some opinion about it. Genetics is really so broad field that I belive one person

Hi, I'm scratching my head as to why I can't use the subset() command to remove one line of data from a data frame. There is just one row (out of 45840) that I'd like to remove and it can be identified using.... > dim(raw.all.clean) [1] 45840 10 > subset(raw.all.clean, Height.1 == 0 & Height.2 == 0) Sample.Name Well SNP Allele.1 Allele.2 Size.1 Size.2

I am trying to get a measure of how R compares in usage as a statistical platform compared to other software. I would guess it is the most widely used among statisticians at least by virtue of it being open source. But is there any study to which I can refer? By asking this list I am not exactly adopting a rigorous approach! Best wishes John John Logsdon

Hi All, I have a problem trying to get a set of columns recognised as a list and can't work out how to do it despite trawling through the mailing list archives, and docs. A short example... to.convert <- NULL n <- 6 for(x in 1:n){ to.convert <- paste(to.convert, paste((2 * x) -1, (2 * x), sep=":"), sep=",") } to.convert <- gsub("^,", "",

Dear R-helpers, I am developing a package named LDehatmap. It depends on the "genetics" package and includes two data files and a demo file. When I'm trying to install it, I get the following messages: * Installing *source* package 'LDheatmap' ... ** R ** data ** demo ** help >>> Building/Updating help pages for package 'LDheatmap' Formats: text html

Dear R wizards, I am seeking advice on graphics in R. Specifically, how to manipulate the size and save a plot I have produced using the LDheatmap library. I confess I am relatively new to graphics in R, but I would greatly appreciate any suggestions you may have. LDheatmap produces a coloured triangular matrix of pairwise associations between 600 genetic markers in my dataset.

> I have an R script that spawns output in the form of an HTML page. This > is done by the R2HTML package. > > Now I want to run the same script using Rcmd BATCH. However, it seems > that it is not possible to use R2HTML in this case. > > My script ends with this error message: > ######################### > Error in dev.print(png, file = AbsGraphFileName, width = Width,

Version 0.2 of the package LDheatmap is now on CRAN. The main function LDheatmap produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot. The revisions to the package are aimed at improving the user's ability to modify and annotate the

Dear R helpers, I am trying to test for linkage disequilibrium (LD) in R between all pairs of loci. Importantly, my loci are microsatellites and have up to 30 alleles per locus. Do you know of any R packages that can either (1) calculate measures of LD directly or (2) test for the presence of LD within a statistical framework? Every package I have run across seems to be only able to handle

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, 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 am having troubles with heatmap(). I have a matrix containing pairwise distance values and I want to plot this matrix with heatmap. I wonder now what distfun is for. Is a distance matrix computed from my initial matrix again and then plotted? cheers, andreas

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, 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, Can someone please guide me towards how to produce "heatmap" output from the output of "hclust" run prior to the actual "heatmap" call? I have some rather lengthy clustering going on and tweeking the visual output with "heatmap" recalculating the clustering every time is not feasible. Thanks, Joh

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