browseGenome width question (rtracklayer)
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Mark Robinson ★ 1.1k
@mark-robinson-2171
Last seen 7.4 years ago
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 at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852
GO hgu95av2 GO hgu95av2 • 569 views
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@michael-lawrence-2759
Last seen 7.4 years ago
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]]
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