Re: [R] Datapoints underneath datapoints Problem

detect points with almost identical coordintes yourself and then change the color of the respective plotting symbol. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University

Re: [R] plotting command trouble

and ylim parameters of the plot function. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute

Re: [R] categorical column to numeric column

-- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675

Re: [R] percent sign in plot annotation

Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel

[R] legend/plotmath/substitute problem

. Any hints are highly appreciated. Thanks Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich 85350 Freising, Germany http://mips.gsf.de/staff/pagel

Re: [R] legend/plotmath/substitute problem

On Thu, Dec 14, 2006 at 06:25:49PM -0500, Duncan Murdoch wrote: On 12/14/2006 5:05 PM, Philipp Pagel wrote: My problem starts, when I want to put more than one series of data in the plot and accordingly need one legend row per data series: year1 = 2001 year2 = 2005 g1 = 1.9 g2 = 1.7 plot

Re: [R] newbie: new_data_frame - selected set of rows

['query2',], ...) scaled_DB$dist3 = distancevector(scaled_DB, scaled_DB['query3',], ...) ... top1 = scaled_DB[rank(scaled_DB$dist1)=5, ] ... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186

Re: [R] comma delimiter comma in text

1, A, 24, The Red House 2, A, 25, King's Home, by the Sea ... Is there a way i can specify to R that King's Home, by the Sea is one word? Yes: It needs to be quoted in the file: 2, A, 25, King's Home, by the Sea cu Philipp -- Dr. Philipp PagelTel

Re: [R] How to increase decimal places

calcualtions are done at full precision, though. Example: a=1/3 a [1] 0.333 print(a) [1] 0.333 print(a, digits=12) [1] 0. For more details have a look at ?print and also at ?options and search for 'digits'. cu Philipp -- Dr. Philipp Pagel

Re: [R] read file problem

2221 9 9.1 5.9792 35.1629.11311 2221 read.table(file, skip = 10) To me it looks like your data is in a fixed-width format. If that is the case you should use read.fwf() instead of read.table(). cu Philipp -- Dr. Philipp PagelTel. +49-8161-71

Re: [R] Read.csv

Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel

Re: [R] one is not one

Goldberg What Every Computer Scientist Should Know About Floating-Point Arithmetic Computing Surveys, 1991 Reprints can be found in many places online - e.g. here: http://www.physics.ohio-state.edu/~dws/grouplinks/floating_point_math.pdf cu Philipp -- Dr. Philipp Pagel

Re: [R] Convert Contingency Table to Flat File

, replace=T) y = sample(c(0,1), 100, replace=T) z = sample(c(0,1), 100, replace=T) # contingency table mytab = table(x,y,z) # flat contingency table as.data.frame( mytab ) cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics

Re: [R] Help on direction of axis in R needed

I'd like to plot things with axes going from the highest to the lowest value You can use the xlim and ylim parameters of the plot function. E.g: x = 1:100 plot(x, x^2) # normal plot(x, x^2, xlim=c(100,0)) # reversed x axis cu Philipp -- Dr. Philipp Pagel

Re: [R] Merge two dataframes of different column length and row length by two columns at a time

? Use merge() cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics

Re: [R] Reading data with blank elements

the option 'fill=TRUE' to tell read.table that you want it to silently pad short rows with empty elements. Another 'popular' reason for funny errors with read.table is the unexpected occurence of quotation or comment characters in the data... cu Philipp -- Dr. Philipp Pagel

Re: [R] how can I delete rows?

%in% set, ] SHCODE COUNTRY NAME WBCTRY X.1. X.2. 3 3 Benin BEN -+ NA 12 12 Congo COG -+ NA 26 26Mali MLI -+ NA cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented

Re: [R] Way to convert data frame to matrix

. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF

Re: [R] Extracting R plots from MS Word

and find the figure in the resulting directory. I'm not sure if and how this works with the new odt format used by openoffice now, but sxw will work. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49

Re: [R] PowerPoint

as photography-like. jpg images of plots tend to suffer from bad artifacts... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan

Re: [R] PowerPoint

On Fri, Jun 23, 2006 at 11:27:00AM -0500, Marc Schwartz (via MN) wrote: On Fri, 2006-06-23 at 18:16 +0200, Philipp Pagel wrote: On Fri, Jun 23, 2006 at 09:21:37AM -0400, Gabor Grothendieck wrote: Note that jpg, bmp and png are in less desirable bit mapped formats whereas eps

Re: [R] how to put the results of loop into a dataframe

example calculation you don't need a loop at all: x = runif(100) y = x+1 z = x+y d = data.frame(x,y,z) cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science

Re: [R] managing data

column of table X is a sub set of the first column of Y. I need to find the matching rows in both tables by looking on their unique identification at the first columns. ?merge cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented

Re: [R] relative frequency plot

(myhist$counts) plot(myhist,main=NULL,border=TRUE,xlab=days,xlim=c(0,6),lty=2) Not exactly clean, though -- we are messing with the myhist object... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71

Re: [R] string vector indices

On Sun, Apr 16, 2006 at 12:26:29AM -0400, Luke wrote: x - a, aab y - a, aa, aab, aabc. Is there any R function to get the indices of y for the elements of x, that is, foo(x, y) will give me the index vector c(1, 3)? match(x, y) cu Philipp -- Dr. Philipp Pagel

Re: [R] simple if statement

Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49

Re: [R] simple if statement

On Fri, Apr 07, 2006 at 09:55:47AM +0200, Philipp Pagel wrote: On Fri, Apr 07, 2006 at 02:58:00AM -0400, Brian Quinif wrote: I tried this years - Freshmen if i==1 years - Sophomores if i==2 What you are looking for is not an if clause but logical indexing: years[years==Freshmen] - 1

Re: [R] load file RData which store in zip file

(file=foo.RData, compress = True) cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute

Re: [R] Remove [1] ... from output

0.09914006 0.8109087 cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics

Re: [R] click on graph and select data points?

Now I want to select the best clustered class, how can I click on the data point, and the program returns the index of that cluster(its class number, or color number)? Have a look at identify() cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept

Re: [R] name of the graphics output

Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187

Re: [R] name of the graphics output

On Tue, Mar 14, 2006 at 01:03:22PM +0100, Philipp Pagel wrote: On Tue, Mar 14, 2006 at 12:55:47PM +0100, Arnau Mir Torres wrote: All the outputs names are file.name.pdf but I want to put a different name for each graphic. you can use paste() to put together the command: file =foo

Re: [R] data import problem

or perl an then just read the table with R. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany

Re: [R] data import problem

1.1024 321 70.05932.1502 ... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute

Re: [R] Semi-log plot in R

On Sun, Mar 05, 2006 at 12:00:19AM +, christophe tournayre wrote: Is it possible to create a semilog plot in R? If you mean a plot with one log-scale axis this is what you want: x = 1:100 y = x^2 plot(x,y, log=y) See ?plot for details cu Philipp -- Dr. Philipp Pagel

Re: [R] How to Import Data

have some kind of separator in your file... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany

Re: [R] random samples

:200 i - sample(1:200, 100) s1 - a[i] s2 - a[-i] cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter

Re: [R] multiple plots problem

on the canvas or open a new device whenever you want a new window. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter

Re: [R] Can R be useful to me?

-- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/~pagel

Re: [R] Problems with postscript output

is trying to be smart about labels getting too close/overlap. Specify the graph to be a little wider and the labels will appear. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF

Re: [R] Frequency table

will give you something like this: as.data.frame(tbl) b Freq 1 (0,20] 17 2 (20,40] 28 3 (40,60] 19 4 (60,80] 15 5 (80,100] 21 Is that what you wanted? cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics

Re: [R] recoding variables

-- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/~pagel

Re: [R] saving a data.frame to \t files

can also add 'quote=FALSE' cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany

Re: [R] Change the result data

Brown 9 14 Red Green 10 14 Red Hazel 11 17 Red Blue 12 26 Red Brown 13 16 Blond Green 14 10 Blond Hazel 15 94 Blond Blue 16 7 Blond Brown Also have a look at reshape(). cu Philipp -- Dr. Philipp PagelTel. +49-89

Re: [R] interesting feature

C3 8 D4 7 E5 6 A1 9 99 B1 10 98 cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter

Re: [R] Read In and Output Postscript file

usefull: Finally R would be capable of producing the wealth of chartjunk other software has offered for decades! Imagine using your corporate logo instead of boring circles or dots for plotting! (OK ok - ouch - don't beat me, please...) ;-) cu Philipp -- Dr. Philipp Pagel

Re: [R] Legend text -- discrepancy between X11 and postscript

placed correctly). This routinely happens to me when using dev.copy2eps. If I use a postscript device to begin with everything is fine. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187

Re: [R] Easiest way to get the mean of a row of a data.frame?

the mean you will find this handy: apply(USArrests, 1, mean) here you can substitute mean by whatever function you'd like to apply to each row. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89

Re: [R] incorporating R into C

. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany

Re: [R] read.table(..)..Help?

a (short) example of what exactly you do, what error messages and warnings you get and what your input file looks like. BTW: read.table returns a data frame so I'm not sure what you mean by using data.frame() later on. cu Philipp -- Dr. Philipp PagelTel

Re: [R] reading data rows

tell us what the goal of all this is and what commands you were using ... cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health

Re: [R] Running R-program as queue jobs

the script on the same machine in both cases? I got burnt a couple of times with different machines running different versions of the OS, non-identical versions of shared libraries etc... cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute

Re: [R] (no subject)

but this sounds like a pretty simple barplot to me. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse

Re: [R] repeat until function

is not much smaller than max-min you may want to generate more numbers than you actually need so unique() leaves you with more results and you don't have to iterate so often... cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics

Re: [R] postscript: font size in text(x,y,label)?

does not work in text()) but using the cex option is a workaround: plot(1:100, (1:100)^2) text(10,1000, foo) text(10,2000, foo, cex=2) cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187

Re: [R] Barplots

in your plot. So you only need to add some offset to your y-values and work out the x-positions: y - c(10,12,15,8) lab - c('*','**','***','*') barplot(y, ylim=c(0,20), space=0.5) x - (0:3*0.5)+1:4 text(x, y+1, lab, adj=0.5) cu Philipp -- Dr. Philipp Pagel

Re: [R] Barplots

to label. Well, maybe you should use the x values returned by barplot (your variable blocks) instead of computing x-positions yourself as I originally suggested. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS

Re: [R] Absolut newbie questions

into the same graph. Have a look at the documentation for plot(), line() and predict(). cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment

[R] weighted rank correlation test?

Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany

Re: [R] Writing and running a R program

editor and run it in R using source(). cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764

Re: [R] r-ish ? how can i improve my code?

... cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany

Re: [R] Getting rows from a dataframe

couple of pages of pretty much every introducory manual. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter

Re: [R] startup file and lambda

On Thu, Oct 09, 2003 at 07:39:58AM -0700, christoff pale wrote: Hi,s there a .Rrc file? so that when R starts up it automatically loads this file? ?Startup will tell you everything you want to know - especially bout the .Rprofile file. cu Philipp -- Dr. Philipp Pagel

Re: [R] extracting the levels of a subset of data

- data.frame(as.matrix( subset(myd, TYPE=='A') )) cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1

Re: [R] How to convert a Rd file into multi html files?

building I initially had the same problem. By looking at other peoples *.Rd files I discovered that you need to separate individual sections of documentation by \eof. Writing R Extensions doesn't seem to mention this, though. hope it helps Philipp -- Dr. Philipp Pagel

Re: [R] big data file geting truncated

'' and ' for quoting by default. Gene descriptions love to contain things like 5' and 3'. = Try quote='' in the read.table call. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National

Re: [R] hi

site: http://www.r-project.org In addition to the official manuals I found the Simple R manual very helpful. It's under contributed documentation. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax

[R] bug plotting dates?

)) R gives me a warning 'parameter ylim couldn't be set in high-level plot() function' but sets the limit as requested, anyway. Any ideas what I'm doing wrong? Is this a bug? cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics

[R] convert factor to numeric

there is no R function to do this in a more readable way. Actually, the behaviour of as.numeric() doesn't strike me as very intuitive. I'm sure it has been implemented that way for a reason - but what is it? cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675