similar to: image quality

Hi, I have been trying to plot density plots using the example on: http://addictedtor.free.fr/graphiques/graphcode.php?graph=139 I used to use this function, but I cannot get any old code or even the example to work. library("geneplotter") require("RColorBrewer") x1 <- matrix(rnorm(1e4), ncol=2) x2 <- matrix(rnorm(1e4, mean=3, sd=1.5), ncol=2) x <-

Hello R help list I have been using the smoothScatter function within the "geneplotter" package to make some graphs using a Sweave Rnw script called via Rscript in a DOS/Windows batch file. The Rscript will ultimately be called by a web service with time-out constraints, hence things need to run as swiftly as possible. The geneplotter package is currently loaded each time R is invoked

Hi, I want to make a plot similar to sm1 (attached). The code I tried is: dcols <- densCols(x,y) smoothScatter(x,y, col = dcols, pch=20,xlab="A",ylab="B") abline(h=0, col="red") But it turned out to be s1 (attached) with big dots. I was wondering if anything wrong with my code. Thanks,Zhengyu -------------- next part -------------- A non-text

Hello, I am attempting to use smoothScatter to plot a heatmap of locations of events in an x-y axis. When I plot the heatmap without passing xlim and ylim parameters, it fills the plot area but the perspective is a bit skewed. I would like to standardize these plots to a uniform window size that does not depend on the range of values in the dataframe. However, when I resize the plot using xlim or

Dear R user, I am using Sweave to write my reports with R code. Unlucly my code take a lot of time to run, and I don't want to run it multiple time, if possible, as I am still developping the tools. It seems that a sweave run does not save the enviroment at the end of the process, is there a way to avoid to lunch multiple time the same commands? maybe it could be possible to store chunck of

Dear R users, I like to plot a matrix A which looks like this: ,1 ,2 ,3 ,4 1, 1 10 100 1000 2, 0.5 0.2 1.0 4.3 3, 0.1 0.2 0.3 0.5 ..... where the 1st row is representing the X-axis values. The subsequent rows should be plotted on the y-axis. I would prefer to use the smoothScatter plotting function of the geneplotter package, but to begin with R I'd be happy to use

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns:

dear all, we am trying to improve the performance of my R code, with the implentation of some function with custom C code. we found difficult to import and export/import data structure such us matrices or data.frame into the external C functions. we already tried the solution from "Writing R Extensions" form the R webpage. do you have any other solution or more advanced documentation

hi BioC, I need to plot a vector of characters on a pdf device, not as a legend, but as in image by itself. I tried text but it is only related to locate text in a plot. what do you suggest? > sessionInfo() R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale:

Hi: Is there a way to get smoothScatter to not clip when I increase the xlim and ylim parameters? Consider the following example: set.seed(17) x1<-rnorm(100) x2<-rnorm(100) smoothScatter(x1,x2) #Now if I increase xlim and ylim notice that the plot seems to be clipped at the former xlim, and ylim boundaries: smoothScatter(x1,x2, xlim=c(-5,5), ylim=c(-5,5)) Thanks. Jen sessionInfo() R

dear all, I have a very simple question but I could not figure out. I need to make plots with grid in the background. something like I old retrive like this a=runif(100)*10 b=runif(100)*10 plot(a,b, pch=20, xlim=c(0, round(max(a))), ylim=c(0, round(max(b)))) vs=seq(0, max(a), 0.5) for(i in 1:length(vs)){ abline(v=vs[i], col="lightgrey") } hs=seq(0, max(b), 0.5) for(i in

Hello, I'm having some trouble getting a good result for a smoothScatter plot. I have some data that I want to log-plot, but when I use smoothScatter the result is not correct. The problem seems to be that with the log="x" argument smoothScatter calculates the bins linearly, so the plot will be skewed towards the right. See for example:

Dear R users, I have a simple problem I cannot solve, but I sure you can help. I have two vector, let say > tmp1 <- c("a", "a", "b", "c") > tmp2 <- c("a", "a", "b", "c", "c", "d") and I want to create a matrix of two column for which I have all the combinations of the same character,

dear all, a simple question, I need to write a function in which I retrive an undetermined number of vector in the function. I solved the problem thanks to this link http://stackoverflow.com/questions/2540232/how-to-allow-multiple-inputs-from-user-using-r so my function will look alike this my_fun <- function(...){ my_list <- lapply(..., function(x){x}) } I need just one more

dear R user, I need a function that download the code of web page as html, to further parse it. something like >site="http://www.R-project.com" >code=function(site) >code !DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <title>The R Project for Statistical Computing</title> <link rel="icon"

On Tue, 18-Dec-2007 at 11:21AM -0500, James W. MacDonald wrote: |> Duncan Murdoch wrote: |> > Yes, I agree. (As an aside, there's actually a capital S in |> > smoothScatter(), and it's a bit of a pain to install, because |> > geneplotter depends on something that depends on DBI, which is not so |> > easily available these days.) |> |> Somehow I always

dear all, I am trying to implement some perl scripting in R to improve the performance of some scripts. I found RSPerl library, but it seems to be quite tricky to import variables. this is a simple example. is there any simpler way to do it? furthermore is there any other available resource to interface the two language? RSPerl seems to be no longer supported and when I load it R complains about

Hello, I have a few questions, regarding the smoothScatter function. I have a scatter plot with more than 500,000 data points for two samples. So, I am wanting to display the density in colors to convince people that my good correlation coefficient is not due to an "influential point effect" and plus, I also want to make my scatter plot look pretty. Anyway ... I have been able to

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