[Gmod-help] Re: [Gmod-gbrowse] wiggle_xyplot smoothing

Wed Jun 2 16:31:30 EDT 2010

Sorry you've had such a miserable time of it. I am hoping to throw out
Bio::Graphics::Wiggle entirely and replace it with a pure-perl
implementation of Bio::DB::BigWig. The naive storage system used in BGW just
doesn't work well across large regions. I recommend Bio::DB::BigWig if at
all possible.

Lincoln

On Wed, Jun 2, 2010 at 3:26 PM, Timothy Parnell <
Timothy.Parnell at hci.utah.edu> wrote:

> Hi Dave,
>
> I identified the source of the problem and possible workarounds/fixes.
>
> The problem stems from the formatting of my wig file. The wig file I am
> using is a variable step wig file that contains the microarray data value
> recorded at just the probe's midpoint. However, when it is converted to the
> binary file, it apparently is converted to a 1 bp fixed step, where all the
> intervening positions are undef. If I use a custom script to pull data out
> of the wib file, it is in 1 bp increments, with undef values at all
> positions intervening the real values.
>
> The problem comes when the zoom level (in bp) exceeds the pixel resolution
> of the track png. The image renderer apparently pulls out a data value at
> every n'th position from the wig file across the region. If the value at
> that position is undef, it simply extends the value from the previously
> found position. This essentially gives the appearance of smoothed data, as
> it may only come across a real value every so often across the region.
>
> There are two workarounds, which I have confirmed works for me. The first
> is to generate a new wig file at 1 bp fixed step by interpolating the values
> between the real number positions. The second is to use Lincoln's new
> adaptor, Bio::DB::BigWig, which fundamentally works differently by pulling
> out features with scores, rather than assuming a fixed 1 bp step interval.
> The BigWig adaptor produces a track indistinguishable from a track produced
> using the SeqFeature::Store database adaptor.
>
> The fix would be in the appropriate Graphics adaptor (wiggle_xyplot.pm????)
> to first toss out all the undef values prior to down sampling for rendering
> the track.
>
> I hope this helps.
> Tim
>
>
> On 6/1/10 5:35 PM, "Dave Clements, GMOD Help Desk" <help at gmod.org> wrote:
>
> Hi Timothy,
>
> I submitted a bug on this.  See
>
>
> https://sourceforge.net/tracker/?func=detail&aid=3010143&group_id=27707&atid=391291
>
> Dave C.
>
> On Tue, May 25, 2010 at 3:10 PM, Timothy Parnell <
> Timothy.Parnell at hci.utah.edu> wrote:
> Hi Dave,
> Yes, I forgot to mention this in my first email. I'm using the latest
> relevant distributions available from CPAN.
>
> GBrowse-2.08
> Bio-Graphics-2.09
> BioPerl-1.6.1
>
> I have not tried checking anything out from the live developer versions.
> Should I try those?
>
> Tim
>
>
>
>
> On 5/25/10 3:54 PM, "Dave Clements, GMOD Help Desk" <help at gmod.org> wrote:
>
> Hi Timothy,
>
> I'm pretty sure this is a a bug.  I know the wig rendering code has been
> touched in the last year or so.  What version of GBrowse is this happening
> in?  I'm hopeful that upgrading will solve this problem.
>
> Dave C.
>
> On Mon, May 24, 2010 at 9:02 AM, Timothy Parnell <
> Timothy.Parnell at hci.utah.edu> wrote:
> Hello,
>
> I'm having issues with the smoothing of wiggle data when rendering a track
> in GBrowse. Specifically, turning smoothing off.
>
> I have the same high resolution microarray data loaded both into a
> SeqFeature::Store database as well as binary wiggle files (via the
> wiggle2gff3.pl <http://wiggle2gff3.pl>  <http://wiggle2gff3.pl>  script).
> Viewing tracks from each data source gives vastly different graphs (see
> attached image). It's most apparent with the histogram plot. It appears that
> the wiggle track is automatically binning the data to smooth it. However, I
> anticipate the "noisy" data as seen in the database track, and it would be
> nice to see it in the wiggle track.
>
> I have set the smoothing option to "none" in the wiggle track
> configuration, but GBrowse appears to be ignoring this line. The smoothing
> occurs at zoom levels above 2 kb, whereas at 1 kb or below the tracks are
> the same. I can pull the data back out of the database and wiggle files
> (using either custom scripts or downloading track data from GBrowse) and the
> data is identical (within expectations of converting the data to 8-bit
> dynamic range).
>
> Is there a way to control the semantic automatic smoothing of wiggle data?
> Is my configuration set incorrectly? Or is this a bug?
>
> My track conf is below:
>
> [sample_chip_wig1]
> feature      = deg_con_ratio_mono1_wig
> glyph        = wiggle_xyplot
> graph_type   = histogram
> height       = 50
> scale        = left
> label        = 0
> autoscale    = global
> bicolor_pivot = zero
> pos_color    = blue
> neg_color    = red
> smoothing    = none
> smoothing_window = 1
> key          = sample_chip_wig1
>
> [sample_chip_db1]
> feature      = deg_con_ratio_mono1_244k
> glyph        = xyplot
> graph_type   = histogram
> height       = 50
> scale        = left
> fgcolor      = black
> min_score    = -2
> max_score    = 2
> label        = 0
> group_on     = display_name
> key          = sample_chip_db1
>
> Thanks for any assistance
>
> --
>
> Timothy J Parnell, PhD.
> Research Associate
> Howard Hughes Medical Institute
> Department of Oncology
> Huntsman Cancer Institute
> University of Utah
> Salt Lake City, UT 84112
>
>
>
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-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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