Hello,
Following the CAGEr tutorial, we can see that "plotInterquantileWidth" function plots four plots for the different conditions showing the histograms of the promoter width. These plots however have different scales in the Y axis. My question is, for an easier comparison between the different conditions, it would be great if you could for example set these Y axis to .20 for all plots. Is is possible do do it using "plotInterquantileWidth"? Are there any other alternatives to achieve this it?

Thank you,

Arturo

There is no ylim argument to this function, so you cannot affect the plots easily. There are really two alternatives. You can either convince Vanja Haberle to add a 'ylim' argument, or you can download the sources and add it yourself. And perhaps send a patch to Vanja if you so desire.

If you want to make the changes yourself and send a patch, the easiest way to do so is to use subversion

svn co --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CAGEr

Then make your changes (the function you want is in CAGEr/R/ExportMethods.R), and then do

svn diff CAGEr/R/ExportMethods.R > patch.txt

And you can then send that to Vanja Haberle, and perhaps she will incorporate it in the package.