similar to: heatmap.2 - change column & row locations; angle / rotate

Hi Chakravarthy, [dont forget to Cc the list for useRs with the same Q.] If you're trying to reuduce the isze of your row or column labels, i think the following arguments of heatmap.2 {gplots} is what you want to adjust- 'cexCol' and 'cexRow'. Specifically on my question that you ask about, i found the BioC forum helpful:

Esteemed R-users, heatmap.2() is yielding an inappropriate key based on my colors and break-points. In the reproducible example below, the key is inappropriate (to me) because- 1. 'Orange' is simply not represented in the key, despite its prescence in the heatmap. 2. The proportions of the key are clearly out, ie., my largest bin, (0.1 - 0.2) is half the range, but this bin (colored

Esteemed useRs and developeRs, I need to create a '3D line plot' (proper name?) of which an excellent example can be viewed here: http://cococubed.asu.edu/images/87a/images/unknown_pleasures.jpg I have some experience using the rgl package to create 3D PCA plots, but have no idea where to start for an image like this. I'd really appreciate suggestions & help on how might

Esteemed R users and developers, How does one 'programatically' list or call objects for use in a function? For example, i thought i could do something better than this: save(A.cwb, B.cwb, C.cwb, D.cwb, E.cwb, F.cwb, file="afile.RData") with something like these- prfxs <- c("A", "B", "C", "D", "E", "F") #**

Esteemed UseRs and DevelopeRs, Just coming to terms with the very attractive proportional venn gernator, venneuler(), but would like to customize a few things. Is it possible to- -suppress all circle labels? -suppress only certain circle labels? -print specific text strings at specified locations within the circles? and unions? -specify circle colors? -specify label font, size & color?

Hi Dimtris and esteemed useRs, I don't understand why i get this error message when attempting to use merge() - > temp <- merge(x, y[,17, drop=FALSE], by=rownames, sort=FALSE) Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any' It should work because: > all(rownames(x[order(rownames(x)),]) == + rownames(y[order(rownames(y[,17,

Esteemed R Users, Would some one be patient enough to explain the variation i see when creating .pdf file output for my plots? FYI- my goal is produce the highest quality .pdf output from the R 'command line' as opposed to using the menu of the acitve graphics window. Im using 32bit WinXP. Session info at the bottom. I have Ghostscript v8.71 installed and in the Path such that

Esteemed UseRs and DevelopeRs, Apologies if this question belongs else where, but it does concern R's package installation/maintenance. How does one start R within Emacs/ESS with root privileges? I tried without success: > M-x sudo R Why i'm motivated to do so: It seems logical to me, as the only user of the PC, to keep my R library consolidated in the universal library rather

Esteemed useRs and Devs, Attempts to update package:rJava to the latest version have failed. See my code and output below. Notably, as suggested here http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing $ sudo apt-get install r-cran-rjava ran successfully without error or warning, but my rJava package is not updated, and remains un-updatable... Greatly appreciate any

Esteemed R-forum subscribers, I'm having a tough time configuring contrasts for my 3-way ANOVA. In short: I don't know how to configure (all) my contrasts correctly in order to specify (all) my comparisons of interest. I succeeded getting my contrasts of interest set up for a simpler 2-way ANOVA based on the fairly intuitive logic of the design col.names. But i'm not able to

Dear R Users, I employed the phyper() function to estimate the likelihood that the number of genes overlapping between 2 different lists of genes is due to chance. This appears to work appropriately. Now i want to try this with 3 lists of genes which phyper() does not appear to support. Some googling suggests i can utilize the Multivariate hypergeometric distribution to achieve this. eg.:

Esteemed UseRs, This must be embarrassingly trivial to achieve with e.g., melt() and cast(): deduplicating records ("pw.X" in example) for a given set of responses ("cond.Y" in example). Hopefully the runnable example shows clearly what i have and what i'm trying to convert it to. But i'm just not getting it, ?cast that is! So i'd really appreciate some ones

Dear UseRs and DevelopeRs It would be helpful to see the color palette available in the venneuler() function. The relevant par of ?venneuler states: "colors: colors of the circles as values between 0 and 1" -which explains color specification, but from what pallette? Short of trial and error, i'd really appreciate if some one could help me locate a "0 - 1" pallette

Esteemed UseRs, I've got many biggish data frames which need a lot subsetting, like in this example: # example eg <- data.frame(A = rnorm(10), B = rnorm(10), C = rnorm(10), D = rnorm(10)) egsub <- eg[eg$A < 0 & eg$B < 1 & eg$C > 0, ] egsub egsub2 <- eg[eg$A > 1 & eg$B > 0, ] egsub2 # To make this clearer than 1000s of lines of extractions with [] # I

Dear List, I'd really appreciate tip's or code demonstrating how i can achieve some common axis labels integrated into a multiple plot. In my example (below), i'm trying to achieve: -a single "Results 1 (Int)" centered & btwn row 1 and row 2; -a single "Results 2 (Int)" centered & btwn row 2 and row 3; and, -a single "Results 3 (Int)" centered

Esteemed R UseRs, Regarding specifying arguments in functions and calling functions within functions: ## beginning ## ## some data ex <- rnorm(10) ex[5] <- NA ## example function Scale <- function(x, method=c("mean", "median")) { scl <- method scl(x) } ## both return NA Scale(ex, method=median) median(ex, na.rm=FALSE) ## both return the median Scale(ex,

Hi, I have a problem with R, after an update: this piece of code: cat("creating resolver data frame\n"); dfG<-cbind(dfG,2^(RGN$G)) dfR<-cbind(dfR,2^(RGN$R)) suddenly, creates values to inf. Is the syntax changed for the ^ symbol in the latest R downloadable version? Kind regards, wilfred -- Dr. Ir. Wilfred Van IJcken Labmanager Genomics Erasmus Center for Biomics,

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 am trying to create a heatmap with some specific requirements. Specifically, I need to be able to center the color-scale around 0, and I need to truncate the data so that a few extreme values do not cause the rest of the heatmap to appear black (on a red/green scale). After reading through and experimenting with heatmap, heatmap.2, heatmap_plus, and heatmap_2, I believe heatmap.2 will

Dear R-Helpers, I have a short question related to heatmap.2 function. I wanted to change the dimension of each cell in the heatmap drawn by this function. here is a reproducible example from the help page library(gplots) data(mtcars) x <- as.matrix(mtcars) rc <- rainbow(nrow(x), start=0, end=.3) cc <- rainbow(ncol(x), start=0, end=.3) hv <- heatmap.2(x, col=cm.colors(255),