search for: smoothscatt

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...

...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 <- rbind(x1,x2) layout(matrix(1:4, ncol=2, byrow=TRUE)) op <- par(mar=rep(2,4)) smoothScatter(x, nrpoints=0) smoothScatter(x) smoothScatter(x, nrpoints=Inf, colramp=colorRampPalette(brewer.pal(9,"YlOrRd")), bandwidth=40) colors <- densCols(x) plot(x, col=colors, pch=20) par(op) But I can't even get the example to work. I have inst...

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: file("http://d...

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 attachment was scrub...

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...

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...

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 th...

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 occurre...

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 forget the capital S and wonder if I have loaded the |> correct package ;-D Maybe you'...

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 r...

...tersted 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 obtain nice plots with the function smoothScatterplot(). My specific problems are the following: *the smoothed scatterplot is somewhat "cutted" inside a rectangular area, specially after trying to fixing the xlim and ylim on the same limits of the shp file. I would like to know if there's a way to overlay the smoothsc.plot to my...

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, xlim=c(100,100000000), ylim=c(100,10000000000), log="xy", pch="." ) the ou...

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 pa...

...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. Tried with the smoothScatter function, but really have no idea how to combine the map with the resulting graph. tx in adv marco -- View this message in context: http://r.789695.n4.nabble.com/smooth-scatterplot-and-geo-map-tp3702374p3702374.html Sent from the R help mailing list archive at Nabble.com.

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 any scatterplot with the given dataset provided in the matrix A. So I tried: plot(A[1,],A[2:3,]) or plot(A[1,],A[2-3,]) both result in : Error in xy.coords(x, y, xlabel, ylabel, log) : 'x...

...stWrite", "fitNorm2", "getPradaPar", "histStack", "plotNorm2", "plotPlate", "readCytoSet", "readFCS", "readSDM", "removeCensored", "setPradaPars", "smoothScatter", "thresholds") importFrom("KernSmooth", "bkde2D") importFrom("RColorBrewer", "brewer.pal") importFrom("utils", "getFromNamespace", "assignInNamespace") importFrom("MASS", "cov.rob") S3meth...

...stWrite", "fitNorm2", "getPradaPar", "histStack", "plotNorm2", "plotPlate", "readCytoSet", "readFCS", "readSDM", "removeCensored", "setPradaPars", "smoothScatter", "thresholds") importFrom("KernSmooth", "bkde2D") importFrom("RColorBrewer", "brewer.pal") importFrom("utils", "getFromNamespace", "assignInNamespace") importFrom("MASS", "cov.rob") S3meth...

...first four columns of. Unfortunately this produces an error stating that plot has created a new plot. I suppose this is the same situation when forgetting "add = TRUE" with plotting functions such as boxplot (as in my code used with "boxplot(x, add = TRUE)" ) or any other (e.g. smoothScatter). Analyzing the partial plot, which can be seen before R rejects my code, I come to the conclusion that add might not be a valid argument for "plot". My questions therefore is, whether there is an option to plot the result of the 1d kernel density estimation to the diagonal of the scat...

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]]

...names=1:3 dummy.df = data.frame(names = factor(names, levels = names), x = seq_along(names), y = seq_along(names)) xyplot(y ~ x | names, dummy.df, xlim = c(1,100), ylim = c(1,100), panel = function(x, y, ...) { x <- X[,x] y <- Y[,y] panel.smoothScatter(x, y ,...) }, layout = c(2, 2, 1), strip = function(..., bg) strip.default(..., bg ="#cce6ff")) In the output, the first plot is represented in the bottom left corner, I would like the plots to be drawn from the top left corner but I cannot find in the Latti...