Re: [R] Width of a plotting point (in inches) in grid package
Hello, I was thinking that was probably the case. I'm creating a series of graphics that contain smaller graphics, and was trying to reduce the bounding box as much as possible with out the plotting points bleeding over to the surrounding features. I could hard code the size of the bounding boxes (or use a creative calculation), but that would be tedious, not to mention what would happen if someone decides they would like to change the plotting point or it's size. ;) The number of predefined types of points available in a pointsGrob is handy, but I also like the idea of using circles or polygons... I might also add that I've just started using the grid graphics system in the last few months, and I'm impressed at how powerful and flexible it is. Thanks! Randy On 2/12/07 2:27 PM, Paul Murrell [EMAIL PROTECTED] wrote: Hi Randall C Johnson [Contr.] wrote: Hello, I'm trying to determine the width of a plotting point (in inches) in the grid package. I naively thought I could create a pointsGrob with only one point and get the width (as tried below), but this results in an object with a size of 0inches (changing cex has no effect). Does anyone have a better approach? Of course, it would be dependent upon the graphics parameters and viewport... The width of a pointsGrob is based on a bounding box surrounding all of the (x, y) locations at which the points are located. It takes no notice of the size of the symbol drawn at the locations. With one point, the bounding box has zero size. The wisdom of this design could be debated ... What do you need the symbol width for? Could you use a circle, rectangle, or polygon instead (all of which calculate their width based on the bounding box of the shape that is drawn)? Paul Thanks, Randy library(grid) pushViewport(viewport()) convertX(grobWidth(pointsGrob(1, 1)), 'inches') [1] 0inches # I think we're measuring the size of the point here... # changing cex has no effect. convertX(grobWidth(pointsGrob(1, 1, gp = gpar(cex = 3))), 'inches') [1] 0inches # If I add a second point, the size should increase... # how big is the plotting point though??? convertX(grobWidth(pointsGrob(1:2, 1:2)), 'inches') [1] 11.1929133858268inches sessionInfo() R version 2.4.1 (2006-12-18) i386-apple-darwin8.8.2 locale: C attached base packages: [1] grid stats graphics grDevices utils datasets [7] methods base ~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick, P.O. Box B Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick, P.O. Box B Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Width of a plotting point (in inches) in grid package
Hello, I'm trying to determine the width of a plotting point (in inches) in the grid package. I naively thought I could create a pointsGrob with only one point and get the width (as tried below), but this results in an object with a size of 0inches (changing cex has no effect). Does anyone have a better approach? Of course, it would be dependent upon the graphics parameters and viewport... Thanks, Randy library(grid) pushViewport(viewport()) convertX(grobWidth(pointsGrob(1, 1)), 'inches') [1] 0inches # I think we're measuring the size of the point here... # changing cex has no effect. convertX(grobWidth(pointsGrob(1, 1, gp = gpar(cex = 3))), 'inches') [1] 0inches # If I add a second point, the size should increase... # how big is the plotting point though??? convertX(grobWidth(pointsGrob(1:2, 1:2)), 'inches') [1] 11.1929133858268inches sessionInfo() R version 2.4.1 (2006-12-18) i386-apple-darwin8.8.2 locale: C attached base packages: [1] grid stats graphics grDevices utils datasets [7] methods base ~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick, P.O. Box B Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] snow's makeCluster hanging (using Rmpi)
Hello everyone, I've been fiddling around with the snow and Rmpi packages on my new Intel Mac, and have run into a few problems. When I make a cluster on my machine, both slaves start up just fine, and everything works as expected. When I try to make a cluster including another networked machine it hangs. I've followed the suggestions at http://finzi.psych.upenn.edu/R/Rhelp02a/archive/83086.html and http://www.stat.uiowa.edu/~luke/R/cluster/cluster.html but to no avail. Everything seems to start up fine using lamboot, but then hangs when making the cluster in R. Making a cluster with 2 slaves seems to work fine, but if I increase the number (to use the networked machines) it hangs again. I've tried networking to another Mac, and also to a machine running Red Hat Linux. Both machines can set up their own local clusters. Does anyone have any ideas? Thanks, Randy sessionInfo() R version 2.4.0 Patched (2006-10-03 r39576) i386-apple-darwin8.8.2 locale: C attached base packages: [1] methods stats graphics grDevices utils datasets [7] base other attached packages: Rmpisnow 0.5-3 0.2-2 ~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick, P.O. Box B Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] snow's makeCluster hanging (using Rmpi)
On 11/7/06 11:28 AM, Ramon Diaz-Uriarte [EMAIL PROTECTED] wrote: On Tuesday 07 November 2006 15:56, Randall C Johnson [Contr.] wrote: Hello everyone, I've been fiddling around with the snow and Rmpi packages on my new Intel Mac, and have run into a few problems. When I make a cluster on my machine, both slaves start up just fine, and everything works as expected. When I try to make a cluster including another networked machine it hangs. I've followed the suggestions at http://finzi.psych.upenn.edu/R/Rhelp02a/archive/83086.html and http://www.stat.uiowa.edu/~luke/R/cluster/cluster.html but to no avail. Everything seems to start up fine using lamboot, but then hangs when making the cluster in R. Making a cluster with 2 slaves seems to work fine, but if I increase the number (to use the networked machines) it hangs again. I've tried networking to another Mac, and also to a machine running Red Hat Linux. Both machines can set up their own local clusters. Does anyone have any ideas? Dear Randy, A few suggestions: a) make sure there are no firewalls; I assume this is actually the case, but anyway; I don't think I have any firewalls running. I checked and they all seem to be disabled... b) what happens if you lamboot outside R (and create a universe with a local and a networked machine) and then you do: lamexec -np 6 hostname? This prints out the host names of each machine as expected. c) are the Rmpi and snow installed in the same directories in the different machines? are there version differences in Rmpi (or Snow) between machines? I've installed the same versions, but they are in different directories... I also tried an example per Luke Tierney's suggestion using only Rmpi, and I get the following error when trying to spawn the Rslaves after starting up with lamboot (outside of R). I tried to use laminfo, but I'm not sure what I'm looking for or how to use the information given... library(Rmpi) mpi.spawn.Rslaves() It seems that [at least] one of the child processes that was started by MPI_Comm_spawn* chose a different RPI than the parent MPI application. For example, one (of the) child process(es) that differed from the parent is shown below: Parent application: MPI_Comm_spawn Child MPI_COMM_WORLD rank usysv (v7.1.0): 0 All MPI processes must choose the same RPI module and version when they start. Check your SSI settings and/or the local environment variables on each node. R(26444) malloc: *** Deallocation of a pointer not malloced: 0x16379a0; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment variable MallocHelp to see tools to help debug Error in mpi.comm.spawn(slave = system.file(Rslaves.sh, package = Rmpi), : MPI_Error_string: unclassified HTH, R. Thanks, Randy sessionInfo() R version 2.4.0 Patched (2006-10-03 r39576) i386-apple-darwin8.8.2 locale: C attached base packages: [1] methods stats graphics grDevices utils datasets [7] base other attached packages: Rmpisnow 0.5-3 0.2-2 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] make error for R-2.3.0
Hello, I'm trying to install R on a linux machine running Red Hat 8. I ran ./configure make and get the following error. I've installed several versions of R (2.2.1 most recently) on this machine and haven't had any problems until now. I wondered if the outdated compiler (gcc version 3.2) was the problem and attempted to install my own, more recent version. I tried gcc versions 4.1.0 and 3.4.6, but still have problems. The output below is using gcc 3.4.6 (my best attempt, but still ending with the same error as gcc 3.2). Any pointers would be appreciated. Best, Randy system: i686-pc-linux-gnu gcc version: 3.4.6 everything seems to be fine up to this point: . . . make[4]: Entering directory `/home/lgd/rjohnson/bin/R-2.3.0/src/modules/internet' gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -g -O2 -std=gnu99 -c Rsock.c -o Rsock.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -g -O2 -std=gnu99 -c internet.c -o internet.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -g -O2 -std=gnu99 -c nanoftp.c -o nanoftp.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -g -O2 -std=gnu99 -c nanohttp.c -o nanohttp.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -g -O2 -std=gnu99 -c sock.c -o sock.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -g -O2 -std=gnu99 -c sockconn.c -o sockconn.o In file included from sockconn.c:34: sock.h:38: error: syntax error before Sock_read sock.h:38: warning: type defaults to `int' in declaration of `Sock_read' sock.h:38: warning: data definition has no type or storage class sock.h:39: error: syntax error before Sock_write sock.h:39: warning: type defaults to `int' in declaration of `Sock_write' sock.h:39: warning: data definition has no type or storage class make[4]: *** [sockconn.o] Error 1 make[4]: Leaving directory `/home/lgd/rjohnson/bin/R-2.3.0/src/modules/internet' make[3]: *** [R] Error 2 make[3]: Leaving directory `/home/lgd/rjohnson/bin/R-2.3.0/src/modules/internet' make[2]: *** [R] Error 1 make[2]: Leaving directory `/home/lgd/rjohnson/bin/R-2.3.0/src/modules' make[1]: *** [R] Error 1 make[1]: Leaving directory `/home/lgd/rjohnson/bin/R-2.3.0/src' make: *** [R] Error 1 ~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick, P.O. Box B Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] make error for R-2.3.0
That's exactly what I needed. thanks to all! Randy On 5/19/06 4:02 PM, Marc Schwartz (via MN) [EMAIL PROTECTED] wrote: On Fri, 2006-05-19 at 15:37 -0400, Randall C Johnson [Contr.] wrote: Hello, I'm trying to install R on a linux machine running Red Hat 8. I ran ./configure make and get the following error. I've installed several versions of R (2.2.1 most recently) on this machine and haven't had any problems until now. I wondered if the outdated compiler (gcc version 3.2) was the problem and attempted to install my own, more recent version. I tried gcc versions 4.1.0 and 3.4.6, but still have problems. The output below is using gcc 3.4.6 (my best attempt, but still ending with the same error as gcc 3.2). Any pointers would be appreciated. Best, Randy SNIP of sock.h related errors Randy, This looks like the same issue that was reported on r-devel back at the end of April for RH 9. Download the latest r-patched tarball and you should be OK. Prof. Ripley made some changes to sock.h that should get around these issues. Unfortunately, they were not reported until after the release of 2.3.0. Download from here: ftp://ftp.stat.math.ethz.ch/Software/R/R-patched.tar.gz It might be time to consider updating your system, since RH 8.0 is not even supported by the Fedora Legacy folks any longer. That means no functional or security updates. Best regards, Marc Schwartz ~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick, P.O. Box B Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R and Power Point
Hello Erin, Have you tried changing the font to a large, bold face font in the GUI preferences? This may take care of the resolution issues without needing to use power point, and give you the flexibility of a live R session. Best, Randy On 2/14/06 1:46 AM, Erin Hodgess [EMAIL PROTECTED] wrote: Dear R People: I'm using R in a time series class. This class is being broadcast live to 2 remote sites via closed circuit TV. My people at the remote sites are having a terrible time seeing the computer screen as it is broadcast(resolution issues). I have decided to put together Power Point slides for the teaching. I am currently saving the R screen as WMF files and inserting them into PowerPoint. While this works, it seems that there might be a simpler method. Does anyone have any suggestions for the Power Point, please? Thanks so much! R Version 2.2.1 Windows Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick, P.O. Box B Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R Graphs in Powerpoint
Have you tried using Keynote? It is a part of iWork and handles pdf files properly (you can resize as many times as you want without loosing image quality). It also will convert to and from Power Point. I would highly recommend it to anyone using OS X. Randy On 10/31/05 6:14 PM, Jarrett Byrnes [EMAIL PROTECTED] wrote: Hey, all. Quick question. I'm attempting to use some of the great graphs generated in R for an upcoming talk that I'm writing in Powerpoint. Copying and pasting (I'm using OSX) yields graphs that look great in Powerpoint - until I resize them. Then fonts, points, and lines all become quite pixelated and blurry. Even if I size the window properly first, and then copy and paste in the graph, when I then view the slideshow, the graphs come out pixelated and blurry. Is there any good solution to this, or is this some fundamental incompatibility that I can't get around? -Jarrett __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ~~ Randall C Johnson Bioinformatics Analyst SAIC-Frederick, Inc (Contractor) Laboratory of Genomic Diversity NCI-Frederick P.O. Box B 1050 Boyles Street Bldg 560, Rm 11-85 Frederick, MD 21702 Phone: (301) 846-1304 Fax: (301) 846-1686 ~~ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
