Question: modifying smoothScatter function
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gravatar for Monica Pisica
10.3 years ago by
Monica Pisica30 wrote:
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]]
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ADD COMMENTlink modified 10.3 years ago by Heidi Dvinge2.0k • written 10.3 years ago by Monica Pisica30
Answer: modifying smoothScatter function
0
gravatar for Heidi Dvinge
10.3 years ago by
Heidi Dvinge2.0k
Heidi Dvinge2.0k wrote:
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 >
ADD COMMENTlink written 10.3 years ago by Heidi Dvinge2.0k
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]]
ADD REPLYlink written 10.3 years ago by Monica Pisica30
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
ADD REPLYlink written 10.3 years ago by Florian Hahne540
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]]
ADD REPLYlink written 10.3 years ago by Monica Pisica30
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