similar to: how to "singlify" entries

Dear list, I hope it is not a FAQ, but I searched the archives and Google, and found nothing. The question is simple : I do not understand why, starting from a symmetrical correlation matrix, heatmap produces an asymmetrical image. Best, Charles -- Charles Plessy, Ph.D. - Genome Science Laboratory The Institute for Physical and Chemical Research (RIKEN) 2-1 Hirosawa, Wako, Saitama 351-0198,

I have read in Paul Murrell's book R Graphics about how to use a bitmap as background for a plot (page 107). Also, I routinely use function read.shape() in package maptools to read maps in shapefile format. Now, I would like to overlay an aerial photograph in .jpg format and a map. I think I could do the alignment manually for each case, but wonder if there is a better, automated way. I notice

Dear all, I wrote the following batch script on a iMac, and ran it on a linux mosix cluster. tu <- read.table("cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshape.table") tu_reshaped <- t(reshape(tu[1:50,], direction="wide", timevar="tu", idvar=c("rna","lib"))) write.table(tu_reshaped, "cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshaped.table")

Dear list, I realised by chance when analysing a 1521862 ? 8 matrix that plotting was much faster when using "." as the argument of `pch'. I was just wondering if there were other ways to get this speed improvement: it is otherwise quite difficult to explore such big matrices, especially given that X11 redraws the plot whenever its window is covered/uncovered by another window, or

Hi, netters, This is probably a rookie question but I couldn't find the answer after hours of searching and trying. Suppose there'a a dataframe M: x y 10 A 13 B 8 A 11 A I want to locate the rows where x >=10 and y="A". I know how to do it to vectors by using which, but how to do it with the dataframe? Thank you very much! Zhihua Li

Hi netters, I have a matrix X of the size (1000,100). The values are from -3 to +3. When I tried heatmap(X, distfun=function(c),dist(c,method="bin"),hclustfun=function(m),hclust(m,method="average")) I got the error message: Error: evaluation nested too deeply: infinite recursion / options(expressions=)? However, if I used default parameters for distfunction:

Hi netters, Suppose I have two data frames X and Y. X has three colnames A, B and C. Y has three colnames A,B and D. I want to combine them into one matrix, joining the rows having the same A and B values (X$A==Y$A and X$B = Y$B). So the resulting dataframe has four variables/columns: A,B,C and D. I was wondering what's the best way to do it in R. Could anyone give me some advice? Thanks!

Hi, netters, First of all, thanks a lot for all the prompt replies to my earlier question about "merging" data frames in R. Actually that's an equivalence to the "join" clause in mysql. Now I have another question. Suppose I have a data frame X with lots of columns/variables: Name, Age,Group, Type, Salary. I wanna do a subtotal of salaries: aggregate(X$Salary,

hi netters, suppose i have a series of objects X1, X2, B1,C1........... they all have the same dimensions. i want to combine into one by using cbind: y<-cbind(X1,X2,B1,C1.....) but i don't want to type the names of these objects one by one. instead, i've put their names into a vector: x<-c("X1","X2","B1","C1",....) i used y<-cbind(x).

hi netters Is there a function in R that can compute the quotient and remainder of a division calculation? such that when 11 is given as the dividend and 5 the divider, the function returns 2(quotient) and 1(remainder). Thanks a lot! _________________________________________________________________ 伱佲伔佈佅伮佋佖 MSN Explorer: http://explorer.msn.com/lccn/

hi netters, i have a dataframe A with several columns(variables). the elements of column M are character strings. so A$M=c("ab","abc","bcd","ac","abcd","fg",....."fl"). i wanna extract all the rows where A$M match some regular expression pattern. for a simple example, let the pattern be just "ab", i wanna subset

hi netters, i have a dataframe TEST like this: Y1 Y2 Y3 X1 4 7 8 X2 6 2 Z X3 8 0 1 i would like to change it to a numeric matrix, replacing "Z" with NA Y1 Y2 Y3 X1 4 7 8 X2 6 2 NA X3 8 0 1 i've tried the function data.matrix but it didn't work. is there any easy way to do this? thanks a lot!

Dear colleages in R, I have earlier been working with R in Linux, where reading in a table containing Scandinavian letters ("?", "?", and "?") in the header as part of variable names has not caused any problem whatsoever. However, when trying to do the same in R running on new MacOS-X (with an Intel processor) with the same original text table does not seem to

Hi all, I recently found out that R does not utilize fully the Duo Core capability when you only run one instance of R. I did some number crunching today and it seems that if I only open 1 R console, it uses 50% of my CPU (either 50-50 or 100-0 on 2 cores). Then, I open the second instance and divide the work into two parts, and run them parallelly, they seems to utilize 100% of my CPU. So, my

hi netters i have a vector NAMES containing a series of variable names: NAMES=c(x,r,z,m,st,qr,.....nn). i wanna fit a regression tree by using the code: my.tree<-tree(y~x+r+z+m+....nn,my.dataframe) but i don't want to type out "x+r+z+m+....+nn" one by one, as there are so many variables. besides, sometimes i wanna put the code in a function. so i need to have the

Hi netters, Now I'm connecting from my local windows machine to a remote linux machine and launch R out there using SSH. When I tried to create grahics, like using plot or heatmap, I cannot see the output. Maybe a new R window displaying the graphics has popped out in the remote machine? Or I need to change some settings for the graphics to display? I don't know. I googled it and

Hi netters, I want to learn a decision tree from a series of instances (learning data). The packages tree or rpart can do this quite well, but the scoring functions (splitting criteria) are fixed in these packages, like gini or something. However, I'm going to use another scoring function. At first I wanna modify the R code of tree or rpart and put my own scoring function in. But it

hi netters Suppose I have a factor X, with 10 elements and 3 levels: A B B C A C B A C C . It is easy to count the number of elements for each level: tapply(X,X,length). Now I have another factor Y, which formed a matrix with X: X| A B B C A C B A C C Y| B B C C C A A A B B I wanna count the number of elements for each of these conditions: when X=A and Y=A; when X=A and Y=B; when X=A and

hi netters, I'm a newbie to R and there are some very simple problems puzzeled me for two days. I've a dataframe here with several columns different in modes. Two of the columns are special for me: column 1 has the mode "factor" and column 2 has the mode "numeric vectors". The values for column 1 are either "T" or "F". I wanna do two things:

Hi netters, I'm using the 64-bit R-2.5.0 on a x86-64 cpu, with an RAM of 2 GB. The operating system is SUSE 10. The system information is: -uname -a Linux someone 2.6.13-15.15-smp #1 SMP Mon Feb 26 14:11:33 UTC 2007 x86_64 x86_64 x86_64 GNU/Linux I used heatmap to process a matrix of the dim [16000,100]. After 3 hours of desperating waiting, R told me: cannot allocate vector of size