Thank you, Tengfei. I have the script handy, as I am would like to generate One Image per Gene Region : I could email it to you shortly, for the moment when you will have more time available. Thanks so much. On Tue, Oct 8, 2013 at 2:02 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > To me this is a very interesting feature request, it's more like multiple > gene regions for tracks, you are talking about 200 regions, make it hard to > fit into one screen, I am thinking about make a function to generate > animation of many gene regions of different tracks, with package > animation, so you could either output the 200 hundred figures into a folder > or go over the regions with Javascript control button in your internet > browser. > > I don't have a function like that in ggbio to support viewing 200 regions > of trakcs, but I could probably provide a scripts to you for that purpose. > > Tengfei > > > On Tue, Oct 8, 2013 at 4:55 PM, Bogdan Tanasa <tanasa@gmail.com> wrote: > >> Thank you all. To add a brief description about my project : >> >> I have a long list of GENE REGIONS (200 regions, each region is of type >> "chr:start-end") and for each region, I would like to display several >> genomic tracks (eg ChIP-seq peaks, gene annotations, etc etc). >> >> I wrote a short script below, using xlim() function. As these 200 regions >> are distributed over 24 chromosomes, it looks that I may have to split the >> data for each of these 24 chromosomes, and run the script for every >> chromosome. Unless you have another suggestions ... >> >> thank you, >> >> bogdan >> >> >> On Tue, Oct 8, 2013 at 1:36 PM, Michael Lawrence < >> lawrence.michael@gene.com> wrote: >> >>> What exactly is the problem? The masking should be harmless; the ggplot2 >>> xlim is masked with a generic that will delegate to it by default. >>> >>> >>> On Tue, Oct 8, 2013 at 1:24 PM, Bogdan Tanasa <tanasa@gmail.com> wrote: >>> >>>> Dear all, and Tengfei, >>>> >>>> I am getting the following message when loading the package "ggbio", >>>> particularly that >>>> "The following objects are masked from ‘package:ggplot2’:" . >>>> >>>> I am especially interested in "xlim" function, to work on a GRange >>>> object. >>>> Any advice ? >>>> >>>> thank you very much, >>>> >>>> --- bogdan >>>> >>>> ------------------------------------------------------------------- >>>> " > library("ggbio") >>>> >>>> Attaching package: ‘ggbio’ >>>> >>>> The following objects are masked from ‘package:ggplot2’: >>>> >>>> geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, >>>> xlim" >>>> -------------------------------------------------------------------- >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@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 > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > [[alternative HTML version deleted]]