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Question: browseGenome width question (rtracklayer)
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gravatar for Michael Lawrence
8.8 years ago by
Michael Lawrence620 wrote:
In rtracklayer 1.3.9, which should be pushed to the web in the next few days, has a 'imagewidth' parameter to the browserView method of UCSCSession, such that session <- browserSession() browserView(session, imagewidth=1000) should give you what you want. Michael On Sat, Nov 8, 2008 at 3:11 PM, Michael Lawrence <mflawren@fhcrc.org> wrote: > Hi Mark, > > I'm glad to hear rtracklayer is working well for you. The rtracklayer API > does not have a way to set the image width. You're probably aware of the > "configure" button and its option for setting the size manually inside the > browser. > > But it sounds like you want something automatic. It would be a relatively > simple addition, but there are many presentation-level options in UCSC, so > I'll have to think about the best way to manage them. It will probably be a > week or so before this lands in the devel version. > > Thanks for the suggestion, > Michael > > > On Fri, Nov 7, 2008 at 11:46 PM, Mark Robinson <mrobinson@wehi.edu.au>wrote: > >> Hi all. >> >> Been using 'browseGenome' to send some data tracks (wig files) to the UCSC >> genome browser. This all works beautifully. For example: >> >> > browseGenome(trackSets(track),segment=genomeSegment(track)) >> A genome browser session of class 'ucscSession' with 1 views and 183 >> tracks >> >> I'm wondering if there is a way to set a width parameter for the image >> that gets displayed within the browser (i.e. the GIF file that UCSC creates >> with all the track). By default, every new window opens with an image of >> width 620 pixels. I'd like to make that something like 1000 pixels if >> possible. >> >> Cheers, >> Mark >> >> >> > sessionInfo() >> R version 2.8.0 (2008-10-20) >> i386-apple-darwin8.11.1 >> >> locale: >> en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] rtracklayer_1.2.1 RCurl_0.91-0 limma_2.16.2 >> [4] GOstats_2.8.0 Category_2.8.0 genefilter_1.22.0 >> [7] survival_2.34-1 RBGL_1.18.0 GO.db_2.2.5 >> [10] graph_1.20.0 annotate_1.20.0 xtable_1.5-4 >> [13] hgu95av2.db_2.2.5 RSQLite_0.7-0 DBI_0.2-4 >> [16] AnnotationDbi_1.4.0 Biobase_2.2.0 >> >> loaded via a namespace (and not attached): >> [1] Biostrings_2.10.0 GSEABase_1.4.0 IRanges_1.0.2 >> [4] Matrix_0.999375-16 XML_1.98-1 affy_1.20.0 >> [7] affyio_1.10.0 cluster_1.11.11 grid_2.8.0 >> [10] lattice_0.17-15 preprocessCore_1.4.0 rJava_0.6-0 >> [13] tcltk_2.8.0 >> >> >> >> >> >> >> >> ------------------------------ >> Mark Robinson >> Epigenetics Laboratory, Garvan >> Bioinformatics Division, WEHI >> e: m.robinson@garvan.org.au >> e: mrobinson@wehi.edu.au >> p: +61 (0)3 9345 2628 >> f: +61 (0)3 9347 0852 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD COMMENTlink written 8.8 years ago by Michael Lawrence620
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