Hi. On Fri, Feb 25, 2011 at 2:44 PM, Kai <wangz...@gmail.com> wrote: > Hi Henrik, > > I read the following thread in the archive (http://groups.google.com/ > group/aroma-affymetrix/msg/dc6eda9aca987a29) where the you guys > discussed how to modify the plotting functions when generating the > Chromosome Explorer plots for CN segmentation results.
Just to be clear; we're not discussing how to change the plot function per se, but the device driver function that generates PNG image files. > > A quote from the post says: "I modified the plotting functions > reducing the line width for regions > to lwd=2 and raw CN pointsize to ces=0.3. Now they look much > better...". > > This is also something what I am trying to do, but I don't seem to be > able to find these "plotting functions" and am not sure on how to > override them. It is plot() for the CopyNumberSegmentationModel class that acts as the main plot function, cf. print(plot.CopyNumberSegmentationModel). But as you can see, it in turn utilizes different functions to plot the data, the annotations etc. From the code you'll find that plotProfile2() is another function of interest, more specifically, plotProfile2.profileCGH() and from there you'll find pointsRawCNs.profileCGH(). BTW, all these functions are in the aroma.core package and you can also access the source code via R-forge in the aroma.* project; https://r-forge.r-project.org/scm/?group_id=429 Since we're not (yet) using namespaces, you can easily override them with your own version. However, I *really* recommend that you instead figure out and solve the problem with your PNG drivers on your cluster. It is not clear what you mean by "bad plots" etc (you can attach example PNGs to this list), but I've heard of it before in R and I think people managed to solve it. Note that there are many different device drivers to generate PNG files in R (e.g. my "png2() wrapper on top of bitmap()") , which is why I created findPngDevice() and ways to specify exactly which you want (as explained in the aforementioned thread). A good approach is to skip the aroma.* framework and instead try to "troubleshoot" this my generating some basic PNG plots using standard R, cf. png(), bitmap(), Cairo, ... You should be able find some that works for you. Also, talk to your sysadm about this. /Henrik > > Just to give you a bit of the background on why I am trying to do > this: I am trying to run "aroma.cn" on a large set of genotyping array > data on an linux cluster. Somehow the plots generated under linux look > far worse than those generated under Windows. For example, each raw CN > data point is much bigger and the segmentation lines are also thicker. > I tried different PNG devices but still cannot get this resolved. So > now I am thinking of modifying the plotting functions to make the > points smaller and line thinner ... > > Thank you very much for your help on this. > > Best, > Kai > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
