[BioC] Modify plot - genas function from LIMMA

Belinda Phipson phipson at wehi.EDU.AU
Mon Oct 21 07:37:18 CEST 2013

Hi Christian

You can use points() to add coloured dots on the figure after you have run
the genas command. The x and y axes are from fit$coeff. For example, you
can identify your significant genes using the match command (or from
decideTests() etc.):


Hope that helps. I wrote the plot function and it is rather crude.


> Hi Christian,
> The short answer is no. The longer answer is 'of course you can!'. And
> thus is the nature of Open Source projects.
> The only argument to genas() that pertains to plots is whether or not
> you want one. The remaining code is all 'hard coded' within the
> function, so you are unable to effect any changes on the results by
> adding extra arguments to the function call.
> However, you have access to the code, and can simply check it out of
> the subversion repository, or if that sounds daunting you can always
> just download the source package and work with that.
> And then all you have to do (easy for me to say) is modify genas() to
> your liking, and then install your modified package.
> An alternative would be to make a really good argument to Gordon Smyth
> for what you want to do, and hope that he buys your argument, and is
> motivated enough to make the changes for you.
> Best,
> Jim
> On Tuesday, October 15, 2013 10:49:21 AM, Christian De Santis wrote:
>> Hi everyone,
>> I am using the function genas from the Limma package to calculate the
>> logFC correlation between some contrasts.
>> genas(fit.contrast, coef = c(2,3), chooseMethod = "Fpval", plot = TRUE)
>> I have isolated the list of DE probes in common between the contrasts of
>> interest and I would like to visualize these probes on the plots with a
>> different colour. Is there a way to do this directly on the plot
>> generated by genas? I am quite stuck on trying to enter the options of
>> the plot argument and impose these parameters. Any help would be very
>> appreciated. Thanks in advance.
>> Regards,
>> Christian
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
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