On Mon, Nov 1, 2010 at 9:11 AM, Paul Shannon <pshannon@systemsbiology.org>wrote:

> Hi Michael,
>
> Thanks for the fix.
>
> My little demo script doesn't run quite right just yet though.  Of my two
> features, only one is rendered.  And the viewLimits appear to be drawn from
> the first features's score, rather then from the viewLimits I supply.
>
> Could you give this a try?
>
>
To fix the scaling, you'll need to specify the autoScale=FALSE parameter.
Otherwise, UCSC will override your view limits.

As far as the missing data, it looks like UCSC is not parsing WIG that
contains multiple "blocks" for the same chromosome. Nothing in the WIG spec
says that this is disallowed. I'll have to email them about this. In the
meantime, you could just force the bedGraph format by passing the format =
"bedGraph" parameter.

Michael


>  - Paul
>
> library (rtracklayer)
> library (GenomicFeatures)
>
> session <- browserSession ('UCSC')
> track.name <- 'demoFeatures'
>
> score <- c (80.3, 99.5)
> chrom.names <- c ('chr1', 'chr1')
> feature.locs <- IRanges (c (201491492, 201491528),  c (201491520,
> 201491607))
> strand <- c ('+', '+')
> name = Rle (c ('feature-1', 'feature-2'))
>
> features <- GRangesForUCSCGenome ('hg18', chrom.names, feature.locs,
> strand, name, score)
> view.range <- GRanges (seqnames='chr1', range=range(feature.locs))
> track (session, track.name, viewLimits=c(80,100)) <- features
>
> view <- browserView (session, view.range, full=c('demoFeatures', 'ruler'),
> dense=c ('chainNetPanTro2', 'chainNetMm9'), hide=trackNames (session))
>
>
>
>
> On Oct 29, 2010, at 4:12 PM, Michael Lawrence wrote:
>
> > I've fixed this in both release and devel, to come with 1.10(11).3.
> >
> > The problem was not related to the viewLimits. Export of WIG was broken
> whenever there were chromosomes in the seqlengths that had no actual ranges.
> Obviously a major bug.
> >
> > Thanks for the report,
> > Michael
> >
> > On Fri, Oct 29, 2010 at 9:44 AM, Paul Shannon <
> pshannon@systemsbiology.org> wrote:
> > Hi Michael,
> >
> > In creating a minimal script to demonstrate my track<- viewLimits
> problem, I got past the 'unused argument' but stuck at the next step.  In
> other programs I have written, I do not see *this* particular problem.
> Something nondeterministic seems to be going on for me.   Maybe you can see
> what I am doing wrong.
> >
> > Here is the 14-line script.  I'll be grateful for any help you can give.
> >
> > library (rtracklayer)
> > library (GenomicFeatures)
> >
> > score <- c (80.3, 99.5)
> > chrom.names <- c ('chr1', 'chr1')
> > feature.locs <- IRanges (c (201491492, 201491528),  c (201491520,
> 201491607))
> > strand <- c ('+', '+')
> > name = Rle (c ('feature-1', 'feature-2'))
> > feature.grange <- GRangesForUCSCGenome ('hg18', chrom.names,
> feature.locs, strand, name, score)
> > view.range <- GRanges (seqnames='chr1', range=c(201491480, 20149120))   #
> slightly larger than the region covered by the features
> > session <- browserSession ('UCSC')
> > track.name <- 'demoFeatures'
> > track (session, track.name, viewLimits=c(80,100)) <- feature.grange
> > stopifnot (track.name %in%  names (trackNames (session)))
> > view <- browserView (session, view.range, full='cytoBand', dense=c
> ('ruler', 'chainNetPanTro2', 'chainNetMm9'), hide=trackNames (session))
> >
> > ---- sessionInfo
> >
> > R version 2.12.0 (2010-10-15)
> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> >
> > locale:
> > [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 GenomicRanges_1.2.0    IRanges_1.8.0
>  rtracklayer_1.10.2     RCurl_1.4-3            bitops_1.0-4.1
> >
> > loaded via a namespace (and not attached):
> > [1] Biobase_2.10.0    biomaRt_2.6.0     Biostrings_2.18.0 BSgenome_1.17.5
>   DBI_0.2-5         RSQLite_0.9-2     XML_3.2-0
> >
> >
> >
> >
> >
> > On Oct 28, 2010, at 4:03 PM, Michael Lawrence wrote:
> >
> > >
> > > On Thu, Oct 28, 2010 at 1:21 PM, Paul Shannon <
> pshannon@systemsbiology.org> wrote:
> > > I have a specific rtracklayer question, and a general S4/help question.
> > >
> > > The specific question:  Michael helpfully suggested  the 'viewLimits'
> parameter to the rtracklayer track method, saying
> > >
> > >     This is another track line parameter, called viewLimits. See
> class?GraphTrackLine.
> > >     track (session, "wiggle", viewLimits = c(0, 100)) <- wiggle
> > >
> > > Indeed, class?GraphTrackLine mentions that parameter.
> > >
> > > But when I call this method (or what I *think* is this method), I get
> this:
> > >
> > >    unused argument(s) (viewLimits = c(80, 100))
> > >
> > > That's my specific question.   How do I supply viewLimits information
> to the track method?
> > >
> > >
> > > Could you please provide a reproducible example? I cannot reproduce
> with a simple test, and really the arguments are not interpreted in a way
> that would result in that error.
> > >
> >
> >
>
>

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