similar to: density plot on a log scale

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

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

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'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:

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 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

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.

Hi, I want to fit a kernel density estimator by bkde of library KernSmooth. I need only the density value at the point 0. I do not understand the following behaviour: > q <- rnorm(100) > bkq <- bkde(q, bandwidth=0.11, gridsize=1, range.x=c(0,0)) Error in 0:L : NA/NaN argument > bkq <- bkde(q, bandwidth=0.11, gridsize=1, range.x=c(-1,1)) > bkq $x [1] -1 $y [1] NA > bkq

Is it possible to call the super class''s version of a function from a subclass? SuperClass = Class.create(); SuperClass.prototype = { initialize: function(){ this.varA = ''''; this.varB = ''''; } } SubClass = Class.create(); SubClass.prototype = (new SuperClass()).extend({ initialize: function(somevar) { this.somevar = somevar; }

Hi all, I have a data frame called "rst", see below: ------------------------------------------------------------------------------------------ # This is a paste able example # In case you don't have "KernSmooth" package installed, please uncomment below line. # install.packages("KernSmooth") library(KernSmooth) rst <- data.frame(hsp = rnorm(23), dal =

Thank you for your reply. I know the x in dpik() means the vector. But I don't know how to import into c() with a huge metadata (>1000). Following is my some try, and the h is: [1] 0.001180569, which seems to be feasible.

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 List, I am trying to plot a grid with an overlayed height. I have a dataframe with four variables: x,y,gridvalue,height. The dataframe has 2.5mio observations (ie grid points), I assign colors through the gridvalue using map_color_gradient thus producing: x,y,gridvalue,height,gridcol as variables of the dataframe. The grid dimensions are 1253 x 2001 (=2507253 data points). My attempts with

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

 Dear Madame or Sir,I am having a problem in combining density-smoothed scatterplot matrices with a plot of kernel destiny estimations of each dimension plotted on the respective field of the diagonal.I have tried following approach using the package "sm" for the kernel density estimation, as well as "MASS" respectively:pairs(myTable[, 1:4],panel=function(x,y, ...){

Hi, I'm in the process of migrating from clang5 to clang10. Unfortunately clang10 introduced a negative performance impact. The cause is an increase of PLT entries from this patch (first released in clang7): https://bugs.llvm.org/show_bug.cgi?id=36370 https://reviews.llvm.org/D43383 If I revert that clang patch locally, the additional PLT entries and the performance impact disappear. This

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]]