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
>>
>> _______________________________________________
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>>
>
>

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