[BioC] modifying smoothScatter function

[Monica Pisica]

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
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>
>
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