This is something on the devel version of geneplotter, where smoothScatter has two formal arguments: xlim and ylim (which do not exist on the stable version). Given the above, matching the arguments in "..." does not work for xlim/ylim, as these two are used as arguments to "zoom" the data. Note that this problem would be fixed by renaming xlim/ylim to something else, like z.xlim/z.ylim. b On Jun 2, 2007, at 11:08 AM, J.delasHeras at ed.ac.uk wrote: > > Hi Rob, > > I tried your example, as I use smoothScatter often too and define my > own limits without problem. Your example _does_ work as intended on my > system... no problem. (?) > >> sessionInfo() > R version 2.5.0 (2007-04-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "datasets" > "tcltk" > [7] "utils" "methods" "base" > > other attached packages: > geneplotter lattice annotate Biobase svSocket > svIO > "1.14.0" "0.15-4" "1.14.1" "1.14.0" "0.9-5" > "0.9-5" > R2HTML svMisc svIDE > "1.58" "0.9-5" "0.9-5" > > Jose > > > > > > > Quoting Rob Scharpf <rscharpf at="" jhsph.edu="">: > >> Hi all, >> >> Is it possible to define your own axis limits in smoothScatter? For >> instance, >> >>> x <- rnorm(1000) >>> y <- rnorm(1000) >>> smoothScatter(x, y, xlim=c(-10, 10), ylim=c(-5,5)) >> >> does not produce the intended result. Suggestions? Session info >> below... >> >> Thanks, >> >> Rob >> >>> sessionInfo() >> >> R version 2.6.0 Under development (unstable) (2007-04-27 r41355) >> powerpc-apple-darwin8.9.0 >> >> locale: >> C >> >> attached base packages: >> [1] "tools" "stats" "graphics" "grDevices" "utils" >> "datasets" >> [7] "methods" "base" >> >> other attached packages: >> KernSmooth geneplotter lattice annotate Biobase >> "2.22-20" "1.15.1" "0.15-4" "1.13.8" "1.15.2" >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > > > -- > Dr. Jose I. de las Heras Email: > J.delasHeras at ed.ac.uk > The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 > 6513374 > Institute for Cell & Molecular Biology Fax: +44 (0)131 > 6507360 > Swann Building, Mayfield Road > University of Edinburgh > Edinburgh EH9 3JR > UK > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

Thanks! I verified that the smoothScatter axis limits work in the 2.5 release (it does). If my patch for the devel release isn't a complete hack, i'll pass it along to Wolfgang. Best regards, Rob On Jun 2, 2007, at 11:08 AM, J.delasHeras at ed.ac.uk wrote: > > Hi Rob, > > I tried your example, as I use smoothScatter often too and define > my own limits without problem. Your example _does_ work as intended > on my system... no problem. (?) > >> sessionInfo() > R version 2.5.0 (2007-04-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United Kingdom. > 1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "datasets" > "tcltk" > [7] "utils" "methods" "base" > > other attached packages: > geneplotter lattice annotate Biobase svSocket > svIO > "1.14.0" "0.15-4" "1.14.1" "1.14.0" "0.9-5" > "0.9-5" > R2HTML svMisc svIDE > "1.58" "0.9-5" "0.9-5" > > Jose > > > > > > > Quoting Rob Scharpf <rscharpf at="" jhsph.edu="">: > >> Hi all, >> >> Is it possible to define your own axis limits in smoothScatter? For >> instance, >> >> > x <- rnorm(1000) >> > y <- rnorm(1000) >> > smoothScatter(x, y, xlim=c(-10, 10), ylim=c(-5,5)) >> >> does not produce the intended result. Suggestions? Session info >> below... >> >> Thanks, >> >> Rob >> >> > sessionInfo() >> >> R version 2.6.0 Under development (unstable) (2007-04-27 r41355) >> powerpc-apple-darwin8.9.0 >> >> locale: >> C >> >> attached base packages: >> [1] "tools" "stats" "graphics" "grDevices" "utils" >> "datasets" >> [7] "methods" "base" >> >> other attached packages: >> KernSmooth geneplotter lattice annotate Biobase >> "2.22-20" "1.15.1" "0.15-4" "1.13.8" "1.15.2" >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor >> >> > > > > -- > Dr. Jose I. de las Heras Email: > J.delasHeras at ed.ac.uk > The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 > 6513374 > Institute for Cell & Molecular Biology Fax: +44 (0)131 > 6507360 > Swann Building, Mayfield Road > University of Edinburgh > Edinburgh EH9 3JR > UK