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
--
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universities for graduate employment*.
94% of our 2012 graduates were in work and/or further study within six
months of graduation.
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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
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$coeff. For example,
you
can identify your significant genes using the match command (or from
decideTests() etc.):
m<-match(sig_genes,fit$genes$Symbol)
genas(fit,coef=c(1,2),plot=T)
points(fit$coeff[m,1],fit$coeff[m,2],pch=16,cex=0.7,col=2)
Hope that helps. I wrote the plot function and it is rather crude.
Cheers,
Belinda
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
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