Hi Florian, This works like a charm ... i cannot believe that i was so wrapped in what i wanted to do that i didn't pay any attention to the "transformation" argument. And believe me i did read the man page. I am properly ashamed. But .... i may still need to have access to the code since i would like to add even more to that poor graph. I am thinking in adding contour lines corresponding to the densities .... Probably it is high time for me to update R. Thanks, Monica ---------------------------------------- > Date: Mon, 10 Aug 2009 15:01:53 -0700 > From: fhahne at fhcrc.org > To: pisicandru at hotmail.com > CC: heidi at ebi.ac.uk; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] modifying smoothScatter function > > Hi Monica, > you might want to take a look at the "transformation" argument. The man > page says: > transformation: function mapping the density scale to the color scale. > > Guess you could simply use this, something along the lines of > smoothScatter(foo, transformation=function(x) > (x-(min(x)))/diff(range(x)) * value of densmax) > > .smoothScatterCalcDensity is not exported from the name space, so you > will have to use the full symbol geneplotter:::.smoothScatterCalcDensity > > Please note that smoothScatter has been moved into R's base graphics > since R-2.10, so you might have to update your function along with your > R at the next release. > Florian > > > > Monica Pisica wrote: >> Heidi, >> >> Thanks. I will try it since i didn't call probably the function in the right way. >> >> I will let know if this solves the problem. >> >> Monica >> >> ---------------------------------------- >> >>> Date: Mon, 10 Aug 2009 21:03:42 +0100 >>> Subject: Re: [BioC] modifying smoothScatter function >>> From: heidi at ebi.ac.uk >>> To: pisicandru at hotmail.com >>> CC: bioconductor at stat.math.ethz.ch >>> >>> HI Monica, >>> >>> I'm afraid I don't know about the smoothScatter colours; there might be an >>> elegant way of handling this. However, are you calling >>> grDevices:::.smoothScatterCalcDensity like in the original function, or >>> just .smoothScatterCalcDensity? A "." in front of a function usually means >>> that it's an internal function that isn't exported by the given package, >>> so you have to call it specifically. >>> >>> Regards >>> \Heidi >>> >>> >>>> Hi, >>>> >>>> I am trying to use the function smoothScatter from package geneplotter. >>>> This is not a problem if i use only one set of variables, but i have >>>> several sets of variables and i would like to compare the plots. Each set >>>> has it's own range of values, so i was thinking to slightly modify the >>>> function to accept a new parameter, for example densmax, and "rescale" the >>>> real densities to the range c(min(dens), densmax). >>>> >>>> In R i've typed the function name to get it's coding and i called the new >>>> function smoothScatt to use in my own scripts. The problem is that R does >>>> not know the function ".smoothScatterCalcDensity" which is used internally >>>> to calculate the density for function smoothScatter so i cannot use my new >>>> function, even if the right libraries are loaded (i hope). Do you have any >>>> suggestions how i can rescale the colors to be able to make comparisons? >>>> >>>> I hope this is the right forum for this question. If not, pleas elet me >>>> know where to address this question. >>>> >>>> Thanks very much for any input and help, >>>> >>>> Monica >>>> >>>> PS. SessionInfo() >>>> >>>> R version 2.8.1 Patched (2009-01-22 r47686) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> >>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>>> States.1252;LC_MONETARY=English_United >>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>>> >>>> attached base packages: >>>> >>>> [1] tools stats graphics grDevices utils datasets methods >>>> base >>>> >>>> other attached packages: >>>> >>>> [1] fields_5.02 spam_0.15-4 geneplotter_1.20.0 >>>> annotate_1.20.1 xtable_1.5-5 >>>> [6] AnnotationDbi_1.4.3 lattice_0.17-25 Biobase_2.2.2 >>>> RColorBrewer_1.0-2 mvoutlier_1.4 >>>> [11] robustbase_0.4-5 >>>> >>>> loaded via a namespace (and not attached): >>>> >>>> [1] DBI_0.2-4 grid_2.8.1 KernSmooth_2.23-1 RSQLite_0.7-1 >>>> _________________________________________________________________ >>>> [[elided Hotmail spam]] >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>> >> _________________________________________________________________ >> [[elided Hotmail spam]] >> >> _______________________________________________ >> 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 >> > > > -- > Florian Hahne, PhD > Computational Biology Program > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-3148 > fhahne at fhcrc.org > _________________________________________________________________ [[elided Hotmail spam]]