[BioC] rtracklayer -- how to hide some default tracks? fine-grained control of track view mode (pack, full, dense, squish...)

Paul Shannon pshannon at systemsbiology.org
Mon Oct 25 18:37:06 CEST 2010

I have climbed what, for me, has been a difficult learning curve with rtracklayer.  Now that I understand it better, I really like it.  It's a very useful package.

I have a few remaining questions about controlling which tracks I see, and what view mode they are in (dense, squish, pack, or full).
How do I implicitly or explicitly hide all tracks, except for a select few, when creating a BrowserView?  And how can I subsequently modify the view mode of selected tracks?

1) When my UCSC browser session has some previously viewed tracks on by default, these remain visible when I create a new view:

    view <- browserView (session, range.to.view, full='exonHits', dense=c ('chainNetPanTro2', 'chainNetMm9')) 

I see these three tracks, plus a half-dozen others left over from previous browsing.

Instead, I wish to tell the browser "hide all tracks except those I explicitly mention', perhaps like this:

   view <- browserView (session, range.to.view, full='exonHits', dense=c ('chainNetPanTro2', 'chainNetMm9'), hide='everythingElse')

2) My second question: how do I communicate the specific view mode when calling the 'trackNames' method?  trackNames will hide everything besides what I explicitly name (a workaround for question 1, above), like this:

      trackNames (view) <-  c ('exonHits', 'chainNetPanTro2', 'chainNetMm9')

But this brings it two problems.   I cannot control the mode of these tracks (dense, squish, pack, full).  And then this method creates a new tab in my browser every time I call it.  (Chrome on OS X 10.6)  So every time I want a particular view, with particular tracks, I need two calls:

    view <- browserView (....)
    trackNames (view) <- (<some track names>)

and I get two tabs, the first of which I always delete.  

I have pored over the browserView and trackNames man pages, peeked at the source, all to no avail.

Any advice?

 - Paul

---- SessionInfo (following a recent update.packages ())

R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] GenomicFeatures_1.1.11             rtracklayer_1.10.0                 RCurl_1.4-3                        bitops_1.0-4.1
 [5] BSgenome.Hsapiens.UCSC.hg18_1.3.16 BSgenome.Mmusculus.UCSC.mm9_1.3.16 BSgenome_1.17.5                    Biostrings_2.18.0
 [9] GenomicRanges_1.2.0                IRanges_1.8.0                      org.Pt.eg.db_2.4.1                 org.Hs.eg.db_2.4.6
[13] org.Mm.eg.db_2.4.1                 RSQLite_0.9-2                      DBI_0.2-5                          AnnotationDbi_1.11.8
[17] Biobase_2.10.0                     RUnit_0.4.26

loaded via a namespace (and not attached):
[1] biomaRt_2.6.0 tools_2.12.0  XML_3.2-0

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