[BioC] Modify plot - genas function from LIMMA

[James W. MacDonald]

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