[BioC] simpleafy plots

[James W. MacDonald]

Hi Assa,

On 4/13/2011 3:13 AM, Assa Yeroslaviz wrote:
> Hi everybody,
>
> Is there a way of changing the default parameters of the plots crated by the
> simpleaffy packge - pairwise.comparison plots.

Yes, but it will take some work on your part.

Hypothetically you could rename plot.pairwise.comparison() in your 
global environment and modify it there, but as you note this gets 
problematic as there are often multiple other functions in the 
simpleaffy namespace that you would have to get as well, and then you 
end up making more work for yourself.

The real way to do this is to download the source for this package, then 
modify the functions (e.g., .pcscatterplot()) required to make your 
changes, then build and install your modified package. Since you are on 
Linux, this is relatively trivial.

If you need guidance on installing packages, please see the 'R 
Installation and Administration' manual, specifically section 6.

Best,

Jim


>
> I want to plot two data aets on the same plot, but they all have the same
> three colors (red, orange and yellow). I tried to assign them different
> colours but I always get an error message, that I have multiple allocations
> for the same parameters.
> The same happens when I tried to set new titles for my X- and Y-axis.
>
> This is how I tried it:
>
>> plot(significant.rma_w,type="scatter") #scatter plot>  plot(significant.rma_d,type="scatter", col = c("purple","blue","green"), add=T) #scatter plotError in plot.xy(xy.coords(x, y), type = type, ...) :
>    formal argument "col" matched by multiple actual arguments
>
> I get a similar error message when trying to set new captions for the axes.
>
>> plot(results.rma_w,significant.rma_w, type="scatter",+ main= "significantly deregulated genes between high and low fractions",+ xlab="high density fraction (w)", ylab ="low density fraction (w)" ) #scatter plotError in plot.default(x, y, xlim = xlim, ylim = ylim, pch = pch, ...) :
>    formal argument "xlab" matched by multiple actual arguments
>
> when doing plot.pairwise.comparison.plot I get only this:
>
>> plot.pairwise.comparisonfunction (x, y = NULL, labels = colnames(means(x)), showPMA = TRUE,
>      type = "scatter", ...)
> {
>      if (type == "scatter") {
>          .pcscatterplot(x, y, labels, showPMA, ...)
>      }
>      else if (type == "volcano") {
>          .volcanoplot(x, y, labels, showPMA, ...)
>      }
>      else if (type == "ma") {
>          .maplot(x, y, labels, showPMA, ...)
>      }
> }
> <environment: namespace:simpleaffy>
>
>
> But when looking for, there is no such real functions to work with as
> .pcscatterplot.
>
>
> I will appreciate any kind of helps
>
> THX
>
> Assa
>
>> R.Version()$platform
> [1] "x86_64-pc-linux-gnu"
>
> $arch
> [1] "x86_64"
>
> $os
> [1] "linux-gnu"
>
> $system
> [1] "x86_64, linux-gnu"
>
> $status
> [1] ""
>
> $major
> [1] "2"
>
> $minor
> [1] "12.2"
>
> $year
> [1] "2011"
>
> $month
> [1] "02"
>
> $day
> [1] "25"
>
> $`svn rev`
> [1] "54585"
>
> $language
> [1] "R"
>
> $version.string
> [1] "R version 2.12.2 (2011-02-25)"
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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