similar to: Strategy for creating a palette...?

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

Dear all, There has been some time since I asked about interpolation in higher (>2) dimensions, and I must admit I failed to write a function to do this myself the last time, but eventually ended up doing it in MATLAB. I tried to translate the MATLAB code, but MATLAB code is so much more opaque than R (S) code, so I failed that too, mainly because I could only get one MATLAB session, I would

Dear all, I have been away for a month, but some time ago, I noted something that was very surprising to me. I think this example illustrates it well: > test <- data.frame(col1 = c(1,2), col2=c(3, 4)) > test col1 col2 1 1 3 2 2 4 > apply(test, 1, function(x) browser()) Called from: FUN(newX[, i], ...) Browse[1]> x$col1 NULL Browse[1]> x[["col1"]] [1] 1

Dear all, I'm a bit confused about the output from functions that generates random values, e.g. rpois. I'm using 0.65.1 on Digital UNIX alphaev6. If I say > rpois(10,5) output is not unexpectedly: [1] 4 6 5 7 6 5 2 2 5 3 but I figured that if I go: > rpois(10,1:10) I would get a 10x10 matrix as output, with random values for each of the vector elements in the row vectors, but

Dear all, Either I'm being totally blind now (as you know, the eyes are the first thing that is blinded :-)), or something is missing in "An Introduction to R". The section heading of section 5.7.1 is "Multiplication, inversion and solving linear equations", and since I was looking for the canonical way of inverting a matrix, this was the place to look. However, I found

Dear all, Me and the Garbage Collector doesn't understand each other... I'm on R-1.0.1 (I have requested an upgrade to the right local people), an osf1 system with an alphaev6 CPU. I have fair amounts of memory to use, but it seems to be used up pretty fast nevertheless. I'm now trying to see what the garbage collector does, I have inserted a gc(v=T) call at a spot in my code. I

Dear all, I have a few files with binary data written by a C program a friend wrote. I allready have program to read these files, Thomas Lumley and Prof Brian D Ripley was kind enough to respond to a question to this list earlier with some code that works perfectly, so this is really no problem, it is more out curiousity. Most of my files consists of 40000 single precision floats, and I figured

Hi folks, I am wondering if the following is possible: I want to control the arguments sent to a function by string variables. For example, instead of > heatmap.2( A, col=greenred(75) ) I would want to have something like: > heatmap.2 ( paste(A, "col=greenred(75)", sep=",") ) Is this possible to do that? Thanks, D.

Dear all, I'm writing a lgrind definition for R. Lgrind is a program to produce pretty program listings for inclusion in LaTeX documents. Does anybody here have any experience with lgrindefs? My definition now looks like this: R:\ :pb=^\d?\p\d<-\dfunction\(\a\):\ :bb={:be=}:cb=\d#:ce=$sb=":se=\e":lb=':le=\e':id=.:\ :zb=@:ze=@:tb=%%:te=%%:mb=%\$:me=\$%:vb=%\|:ve=\|%:\

Dear all, I'm writing a lgrind definition for R. Lgrind is a program to produce pretty program listings for inclusion in LaTeX documents. Does anybody here have any experience with lgrindefs? My definition now looks like this: R:\ :pb=^\d?\p\d<-\dfunction\(\a\):\ :bb={:be=}:cb=\d#:ce=$sb=":se=\e":lb=':le=\e':id=.:\ :zb=@:ze=@:tb=%%:te=%%:mb=%\$:me=\$%:vb=%\|:ve=\|%:\

Dear all, I think I must be going crazy.... If I do > mean(rpois(1000000, 14)) I get: [1] 13.50420 and again: > mean(rpois(1000000, 14)) [1] 13.49896 > mean(rpois(1000000, 14)) [1] 13.50161 > mean(rpois(1000000, 15)) [1] 14.49250 > mean(rpois(1000000, 15)) [1] 14.49897 > mean(rpois(1000000, 14.5)) [1] 13.99689 > mean(rpois(1000000, 14.5)) [1] 13.9963 This was on a platform

Dear all, I have been trying to understand what runif() is telling me. I am generating lots of numbers (billions and billions (wow, I''ve dreamed about saying that for many years... :-) ), for a distribution that has the following quantile function: 1 / (2 * sqrt(1 - p)) (that is, the distribution has a lower cutoff) As you can imagine, this has rather heavy upper tail. I was

Using the heatmap.2 function, I am trying to generate a heatmap of a 2 column x 500 row matrix of numeric values. I would like the 1st column of the matrix sorted from the highest to the lowest values - so that the colors reflected in the first column of the heatmap (top to bottom) go from red to green. After sorting the matrix (z), I tried the following command, but the data remains

Dear all, I have an image that I need to filter, and so I'm looking for a method to convolve it with a matrix. If I understood the docs for convolve correctly, it only works in 1D (and I have tried to convolve, it didn't look good). So, I wondered if anybody have implemented 2D convolution in R, or have any good advices to share (beyond having a look at mvfft), before I go hacking?

Dear all, I'm a bit concerned about underflow problems. Such problems typically occur when two almost equal numbers are subtracted. I was wondering if R has any mechanisms for warning users about potential problems, or if any policy has been developed? To check, I just did: > 1.0000000000000001 - 1 [1] 0 > 1.000000000000001 - 1 [1] 1.110223e-15 > 1.00000000000001 - 1 [1]

Dear all, A looong time ago, Witold Eryk Wolski asked here why there wasn't a log="xy" parameter to the hist() function <URL:http://www.R-project.org/nocvs/mail/r-help/2001/0267.html>, and Prof. Ripley responded that a loglog histogram does not make much sense, and that one should use a better density estimate if one seeks to plot log density. I understand the point and I

Dear all, Is there a simple way to add a qqline to the Q-Q plot plot.lm() produces for which = 2? If not, I might write one, but how should this preferably be implemented? Make qqline() generic and add a qqline.lm() method? Add an argument to plot.lm()? Have plot.lm() output something invisibly that qqline() can chew directly? Have plot.lm() output something invisibly that abline() can chew?

Dear all, I have just finished my thesis titled "Gravitational Microlensing of Quasar Clouds", and the following paragraph appeared in my "Acknowledgements": "I would like to thank the authors of R and the R core team for their great skill and dedication in developing this software, and to all the members of the R-help mailing list, especially Brian D. Ripley,

On 8 Nov 2000, Peter Dalgaard BSA wrote: >Done... Great! >(This kind of behaviour has been observed on various platforms and >various compilers, sometimes getting stuck around 15.15 and sometimes >around 14.5. Others report no problems. Very strange. I've seen one >case where it apparently shifted from one regime to the other.) Yes, it does that here too.... The following is

Dear all, I am just wondering if anybody has implemented a function that can give a piecewise linear interpolation in more than 2 dimensions? I have looked at the akima package, but I would rather like a piecewise linear interpolation rather than a spline and while it did the job quite satisfactory for 2 dimensions, I need to interpolate in at least three dimensions. If anybody has implemented