similar to: Determining Legend for smoothScatter

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 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 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'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:

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 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-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

Hello, I have a 32 GB RAM Mac Pro with a 2*2.4 GHz quad core processor and 2TB storage. Despite this having so much memory, I am not able to get R to utilize much more than 3 GBs. Some of my scripts take hours to run but I would think they would be much faster if more memory is utilized. How do I optimize the memory usage on R by my Mac Pro? Thank you! Kurinji [[alternative HTML version

Hello, I have one column in my dataframe that has gene names of interest. Unfortunately, due to the fact that some probes lie between two genes or two transcripts of a gene, it looks something like this - FAM81A LOC283050;LOC283050;LOC283050;ZMIZ1 PINK1;PINK1 MRPL12;MRPL12 C1orf114 MMS19;UBTD1 I would like to know how to get a list with all the names with no semi-colons and removing the

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

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 all, Considering this simple example of hexbinplot: mixdata <- data.frame(x = c(rnorm(5000), rnorm(5000,4,1.5)), y = c(rnorm(5000), rnorm(5000,2,3)), a = gl(2, 5000)) fig <- hexbinplot(y ~ x | a, mixdata) print(fig) update(fig, colramp = BTC) produces a bad (non-updated) legend. Compare it with: hexbinplot(y ~ x | a, mixdata, colramp = BTC) What

Hi everybody, just arrived at R and immediately I got a problem. Here's my script: setwd("C:/Users/Tom/Eigene Tools/Programming/R/Data") blast_hits<-read.table("blastHit_covLenght.txt", header=T) blast_hits <- as.matrix(blast_hits) numerical1<-data.matrix(blast_hits, rownames.force = NA)

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

R listers: I have been foiled by plotmath! (in R 2.01,Windows 2000) The task: Plot a normal density and label the ticks as mu - 3 sigma, mu - 2 sigma, ...., mu + 3 sigma, where the mu's and sigmas appear as Greek symbols, of course. The following code does this: x<-seq(-3,to=3,by=.01) y<-dnorm(x) plot(x,y,type='h',col='lightblue',axes=FALSE)

Hello everybody, I'm trying to create my own color palette on R, in order to interpolate some different temperature data on different maps (daily means, seasonal means,...). I would like to create a color palette which works for each map, so I need a color palette between -40 and +40?C. Sometimes my data for one map range from -10 to +20, sometimes from 10 to 30, etc... but always between

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 users, I would like to create several forestplots with the same X axis, so, if you were to look at the plots lined up all the X axes would be identical (and the different plots could be compared). Here is one version of code I've used: mytk10<-c(0.1, 0.5, 1, 2, 5, 10) pdf(file = "myfile.pdf", pointsize = 7, paper="letter", width=6, height=9)

Hi Dan, Hi All, I read the below post. I am wondering how do I know which "keys" are available, e.g. "core.r" and "pre". Where kind I find the definition of what can be adjusted and which "words" to use? Kind regards Georg > Gesendet: Donnerstag, 08. Juni 2017 um 16:16 Uhr > Von: "Nordlund, Dan (DSHS/RDA)" <NordlDJ at