Hey James, So sorry for the late reply, in case I forget, you can also leave your question/feedback ingithub issues page backlog <https: github.com="" tengfei="" ggbio="" issues="">. I will work on those backlogs when I got time. Are you looking for a normalization cross samples for coverage? Unfortunately, it's not built-in yet. But I am re-work on autoplot() for bamfile list for particular regions now, I will think about give options on normalization considering the library size. Or more flexible, you could use your own method to do normalization on the raw RleList, then autoplot will provide better/faster graphics for RleList after the improvements. This new features will be implemented in devel branch. Let's keep in touch. cheers Tengfei On Wed, Jul 9, 2014 at 5:26 PM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > Hi, > > Is there an easy way to adjust the coverage plots for library size? As an > example, if I do > > library(ggbio) > library(Rsamtools) > which <- GRanges("chr12", IRanges(29358072, 29367039)) > bfl <- BamFileList() > p1 <- autoplot(TxDb.Mmusculus.UCSC.mm9.knownGene, which=which) > p2 <- autoplot(bfl, which=which) > c(tracks(p1), p2) > > I get almost what I want, but the plot is misleading because the coverage > is dependent on the library size, and I would like to account for that > fact. Is there some way to incorporate the library size in the computation > of the coverage? In other words, I would rather plot coverage/million reads > or similar. > > Thanks, > > Jim > > > -- > 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 > -- Tengfei Yin, PhD Product Manager Seven Bridges Genomics sbgenomics.com One Broadway FL 7 Cambridge, MA 02142 (617) 866-0446 [[alternative HTML version deleted]]