similar to: smoothScatter problems

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 <-

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 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

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

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

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

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:

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 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.

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,

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

I wish to save a scatter plot comprising approx. 2 million points in order to include it in a LaTeX document. Using 'pdf(...)' produces a file of size about 20 MB, which is useless. Using 'cairo_pdf(...)' produces a smaller file, around 3 MB. This is still too large. Not only that the document will be too large, but also PDF viewers choke on this. Moreover, Cairo has problems

There is an issue with the default svg device on a centos workstation that I am using. It does not result in an error, but it produces malformed svg images. Exactly the same script works just fine on an ubuntu box. On Ubuntu I am using R binary that comes with maverick, on centos I am using the latest R binary from EPEL. Other than that both boxes are pretty clean, with only the dependencies

Hello everybody, I'm trying to understand how to draw a smoothed scatterplot on a geographic map with R. Have a dataframe with point locations (long, lat) and was able to simply plot these points on a shp map by using the maptools package. However, instead of having simply the raw points on the map, I would like to have a "smoothed" scatterplot of the same superimposed on the map.

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

Good day, I'm having a few problems with Samba 3.0.2a, specifically involving the username character substitute, %u. For some reason, Samba resolves the %u character wrongly when used in the "path" parameter, where it resolves it as the guest account. However, the server in question has "map to guest" set to never and both "guest ok" and "guest only"

SPSS seems to have changed its default datafile format, resulting in issues for read.spss(). In Windows this results in a warning, in Debian the import completely fails: Debian (R version 2.8.0 (2008-10-20) i486-pc-linux-gnu, foreign_0.8-29) > read.spss("/home/jeroen/samples/Tomato.sav") Error in iconv(names(rval), cp, "") : unsupported conversion from 'CP65001'

> From: Eric Christopher > Subject: Re: [LLVMdev] How to associate extra comments to a > MachineInstruction ? > > Should be spelled like this yes? > > Asm->OutStreamer.AddComment("foo") > Asm->EmitFoo(); > > -eric That should work at the moment that you are emitting the instructions. But what would you do when you are manipulating a

Hi Chris, I've properly started looking into this yesterday. NSD definitely shouldn't crash, still working on that. However, the provided zone is invalid too(?) I'm not the foremost expert on NSEC3 (or even DNSSEC), but is seems an NSEC3 is missing for bar.foo.com. Empty non-terminals should still have an NSEC3 RR. (Of course, the delegation point should be at bar.foo.com. too and