similar to: C/C++

Hi, I clustered a distance matrix and would like to draw it using plot.hclust or plot.dendrogram. The dendrogram is not informative because I have a few extremely small dissimilarities in the distance matrix (e.g. 0), but most of the other distances are in the range 1e10+-5000. I would like to show the tree only for the height of 1e10+-5000 but unfortunately their are no parameter like

Hi, Would like to use to the hexbin package to plot a 2D hist - because it looks really _cool_. My problem is related to drawing a pdf hexbin graphic in series of other graphics. All other figures have a par(mar=c(3.2,3.2,1,1)). So the gplot.hexbin figure in this series looks a little alienated? Was trying a to specify the _mar_ using par, viewport, hexViewport etc. a little. My question. How

Hi, hres <- hclust(smatr,method="single") hresd<-as.dendrogram(hres) as.dendrogram(hres) `dendrogram' with 2 branches and 380 members total, at height 2514.513 plot(hresd,leaflab="none") #<-error here. #the plotted dendrogram is incomplete. The x axis is not drawn. #The interested reader can download the save(hresd,file="hres.rda") #from the

Hi, I want to draw a scatter plot with 1M and more points and save it as pdf. This makes the pdf file large. So i tried to save the file first as png and than convert it to pdf. This looks OK if printed but if viewed e.g. with acrobat as document figure the quality is bad. Anyone knows a way to reduce the size but keep the quality? /E -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare

Hi, I am using R to plot the graph and the problem I am facing with my graph is that I have lots of points concentrated in one area and It is creating a visualization challenge. Is there any commands in R I could use to solve this problem. Even if there is no command, do you know how I could tackle this problem...(I want to separate these points so I could see each of them...) Any help is much

Hi- I used to use "<<-" to do assignment inside a class method, and just found that now it is broken in R 2.0. For example, the following code ----------------------------------------------------------------------- setClass( "myclass", representation(x="numeric") ) setGeneric("incrXByOne", function(obj) standardGeneric("incrXByOne"))

Hello, am I using 'setIs' in the correct way in the subsequent (artifical) example? Do I have to specify explicit 'setAs' for 'list' and 'vector' or should this work automatically, since "getClass("List1")" states an explicit coerce also for these classes. I'm working with R 2.0.0 Patched (2004-10-06) on windows 2000. Thanks for your

I have an S4 class with a slot of class "array", and in upgrading to 2.0.1 (from 1.9.1) I have encountered a change in behaviour. This causes me some difficulties if I want to allow 2-dimensional arrays in the slot. The following (in 2.0.1) illustrates the point: > setClass("foo",representation("array")) [1] "foo" > a <-

I have question regarding package installation. What is the difference between check, INSTALL, build and build --binary, which imply which and what order does one normally perform them? I have been trying: R CMD build /mypackage R CMD check /mypackage R CMD build --binary /mypackage in that order but wanted to check that this is right. Also, what portion of the check process can be run

Hello, I'm hoping that there is an easier way to rename columns in a data frame other than by using the names() assignment, which requires you to type in all the column names at once for a data.frame, in the case that I simply want to rename a single column in a data frame. Also, is there an easy way to move columns in a data frame around relative to the other columns? Thanks in

This seems like a bug to me. Can someone verify this? First we define a function f that returns its second argument and lapply it to 1:2 using 9 as the second argument and all seems well. Note that "{" as a function does the same thing as f, as illustrated with f(1,9) and "{"(1,9); however, when we attempt to use "{" in the very same way we used f in lapply,

I have been struggling with this problem for a while and I hope someone could help me. Or if someone could point me to a section in the manual I would be grateful. x <- "my" plot(1:10, main=expression(paste( x, Delta, "values" ))) Q : How do I get the title to say "my (triangle symbol) values" ? The following trial-and-error produced mainly errors :

Hi, How to add values to an array at any position. Asking because of the following: e.g. y<-c(0.1,NaN,0.2,NaN) #or data frame x<-na.omit(y) take some columns from x and do some computation with functions which do not allow NaN 's. After the computing add NaN's at positions stored in attr(x,"na.action") of the result vector. /E -- Dipl. bio-chem. Witold Eryk

Hi, Is the ordering of the values returned something on what I can rely on, a form of a standard, that a function called unique in R (in futher versions) will return the uniq elements in order of they first occurcence. > x<-c(2,2,1,2) > unique(x) [1] 2 1 Its seems not to be the standard. E.g. matlab >> x=[2,2,1,2] x = 2 2 1 2 >> unique(x) ans =

Hi, Executing the following code causes the prompt to enter browser() mode. >dd<-as(Npatrick1,"list") Called from: as(Npatrick1, "list") Browse[1]> R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.0 beta (2004-09-20), ISBN 3-900051-07-0 Some addtitional info about Npatrick1 > is(Npatrick1) [1] "Massvectorlist"

Hi, Please consider the following trivial example. In the sample code I first define a class MVCa using composition. This class contains a slot of type list. Next I define an inheritance relation using the function setIs -> MVCa "is a" list. Then I define a function printlength which prints the list-length which is defined for the type "list". If I call this function

Hi, Drawing a legend I would like to be able to specify the color of boxes which are drawn if fill or density is specified. eg. legend(0,40000,c("raw","LR/PR-TPS"),fill=c(1,2),col=c(1,2),density=c(20,20),angle=c(-20,45),bty="n") Currently the color of the boxes -- border is always black and can *not* be changed. To get this option only a *minimal* change is

I have a 20x3 matrix as follows: > m <- replicate(3, matrix(rnorm(20),20,1)) I need to compute, say, 95th and 99th percentiles of each column such that the resulting matrix becomes 2x3 with each row representing the respective percentile. My "best effort" is to compute one column at a time as follows: > quantile(m[,1], c(0.95, 0.99)) To do the same for columns 2 and 3, I

Hi! I am installing R in non standard directory. ./configure --prefix=/non/standard/directory The installation works fine. But after starting R i get .libPaths() /usr/lib/R/library but they cant be there of course! Have I to set some additional switches during config? Eryk Dipl. bio-chem. Eryk Witold Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel:

hello I am returning to some libraries that I had previously customised by amongst other things adding additional functions. I had simply typed these new functions into the file in library/R/thelibrary. These however do not seem to be loaded now as they previously were under older versions of R. What's changed and what do i need to do? Thanks Stephen