[BioC] modifying smoothScatter function

Heidi Dvinge heidi at ebi.ac.uk
Mon Aug 10 22:03:42 CEST 2009


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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