[BioC] modifying smoothScatter function

[Monica Pisica]

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
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>>>>
>>>
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>
>
> --
> 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
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