smoothScatter axis limits
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Rob Scharpf ▴ 250
@rob-scharpf-1931
Last seen 7.7 years ago
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"
annotate geneplotter annotate geneplotter • 1.6k views
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@wolfgang-huber-3550
Last seen 4 months ago
EMBL European Molecular Biology Laborat…
Hi Rob , currently this is not implemented, but it would not be difficult to do that (have a look at the function definition and that of geneplotter:::.smoothScatterCalcDensity). Patches are welcome :) For now, a pragmatic way to circumvent this is to subset x and y in your code example to remain within the intended ranges before calling smoothScatter. Best wishes Wolfgang Scharpf ha scritto: > 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" >
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@jdelasherasedacuk-1189
Last seen 6.8 years ago
United Kingdom
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
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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
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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
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