similar to: SmoothScatter plot range issue

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, 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

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

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

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:

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

Hello, I have found that in smoothScatter it is not possible to reverse the axes plotted (R version 2.9.0) .   It appears that this arises from the hard coding of xlim and ylim in smoothscatter.R in the lines : x <- x[ xlim[1] <= x[,1] & x[,1] <=xlim[2], ]   (line  number 25) and x <- x[ ylim[1] <= x[,2] & x[,2] <= ylim[2], ]  (line number 31) This results in a x

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

Dear all, I am using the smoothScatter function in base R for a plot - Lab.palette.both <- colorRampPalette(c("darkblue","lightblue","red","yellow"), space = "Lab") smoothScatter(X24fresh.sorted[,c(13,10)], colramp = Lab.palette.both) I understand that my yellow colored points represent highest density, red lower, lightblue even lower etc.

dear all, I am writing a sweave documentation for my analysis, and I am plotting huge scatter plot data for microarray. unlucly this take a lot of resource to my pc because of the quality of the image which is to high (I see the PC get stuck for each single spot). how can I overcome this problem? is there a way to make lighter image? john [[alternative HTML version deleted]]

Hello, I am searching for the best method to plot two variables with points whose output color depends on the size of a third variable. For example, the darkness of the x-y point would increase incrementally based on the size of the z value, similar to the colramp parameter in geneplotter. This would be analagous to symbols(), except changing the selection from the color gradient rather than the

Dear R-devel, my Bioconductor EDASeq package has a function MDPlot that uses the smoothScatter() function from the graphics package. When I test this package on travis-ci.org (R CMD check) I get the following error (which I don't get on my machine nor on the Bioconductor build system). * checking examples ... ERROR Running examples in ?EDASeq-Ex.R? failed The error most likely occurred in:

Hello everybody, I'm here with a question concerning obtaining a greographical map with a smmothed scatterplot overlaying the intersted regions. My data are a set of opints, represented by long, lat coordinates. As far as the map is concerned, a shp file of Europe without countries borders (only coastal outlines) with the limits at lat 35N-60N long 15W-30E. Until now, I was only able to

I'm working with a large dataset - large enough that when I do a scatter plot the points all blur together, so I want to plot their density by color - a heat map or something like that. I've used smoothScatter for tasks like this, but the problem is that my current dataset really only looks good on a log-log scale. When I do the following command smoothScatter( data,

Hi, I have a set of genes and its chromosomal physical position in a text file. I want to view those genes in the chromosome using R package GenePlotter. Could any one please tell how to view this. Thanks in advance. Yours sincerely, S.Mahalakshmi [[alternative HTML version deleted]]

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:

I downloaded: http://www.bioconductor.org/data/metaData/hgu95av2_1.7.0.tar.gz described as: Package: hgu95av2 Title: A data package containing annotation data for hgu95av2 Version: 1.7.0 Created: Wed Jan 12 16:57:23 2005 Author: Lin,Chenwei Description: Annotation data file for hgu95av2 assembled using data from public data repositories Maintainer:

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

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =