[Bioperl-l] [Gmod-gbrowse] xyplot data alignment problem?

Fri Dec 15 16:02:27 UTC 2006

This is very embarassing for me, particularly since I spent a lot of time
validating that Bio::Graphics was working properly before the 1.5.2 release
went out. How long before there is a 1.5.3 release? How about a 1.5.2.1release?

Lincoln

On 12/14/06, Lincoln Stein <lincoln.stein at gmail.com> wrote:
>
> Hi All,
>
> I'm afraid that the xyplot glyph that is in the recent bioperl release has
> an error that causes the content to be printed to the right of the correct
> position. Unfortunately this wasn't caught before the release because the
> glyph was only tested on very large (whole genome) features.
>
> You will need to do a CVS update to get a fixed version from bioperl-live.
> A future bugfix release of gbrowse will patch this glyph for you
> automatically.
>
> Lincoln
>
> On 12/12/06, Kara Dolinski <kara at genomics.princeton.edu> wrote:
> >
> > Hi,
> > I'm having a problem getting features and an xyplot properly aligned in
> > Gbrowse.  For example, see this page:
> >
> > http://tinyurl.com/ylbq3q
> >
> > The feature in the "CENPK SNPs" track should actually be around the peak
> > of the graph in the "CENPK prediction signal" xyplot  ie. the SNP
> > feature is at position 79, and the xyplot axes and data should span from
> > 61 - 95.  However, as you can see, the data in the xyplot are oddly
> > separated from the axes (which seem to be in the correct place), with the
> > data shifted over to about position 120-155.
> > This occurs elsewhere, not just at the ends of the chromosomes.
> >
> > When I zoom to ~80 bp, all is well, see:
> >
> > http://tinyurl.com/yzav8k
> >
> > The relevant snippets from the GFF and the config files are below.
> >
> > Thanks!
> > Kara
> >
> > GFF:
> >
> > chrI SNPScanner
> > CENPK_GRAPH 61 95 41.9883 . . ID=CENPK_all_peaks;Name=CENPK_peak0;PEAK=peak0;Note=score
> > is 41.9883
> > chrI SNPScanner
> > CENPK_CALL 79 79 41.9883 . . ID=CENPK_all_peaks;Name=CENPK_peak0;PEAK=peak0;Note=score
> > is 41.9883
> > chrI SNPScanner
> > CENPK_SCORE 61 61 2.24506 . . ID=CENPK_all_peaks;Name=chrI61;PEAK=peak0;Note=score
> > is 2.24506
> > chrI SNPScanner
> > CENPK_SCORE 62 62 3.26837 . . ID=CENPK_all_peaks;Name=chrI62;PEAK=peak0;Note=score
> > is 3.26837
> > chrI SNPScanner
> > CENPK_SCORE 63 63 1.39938 . . ID=CENPK_all_peaks;Name=chrI63;PEAK=peak0;Note=score
> > is 1.39938
> > chrI SNPScanner
> > CENPK_SCORE 64 64 1.4039 . . ID=CENPK_all_peaks;Name=chrI64;PEAK=peak0;Note=score
> > is 1.4039
> > chrI SNPScanner
> > CENPK_SCORE 65 65 9.16134 . . ID=CENPK_all_peaks;Name=chrI65;PEAK=peak0;Note=score
> > is 9.16134
> > chrI SNPScanner
> > CENPK_SCORE 66 66 10.1413 . . ID=CENPK_all_peaks;Name=chrI66;PEAK=peak0;Note=score
> > is 10.1413
> > chrI SNPScanner
> > CENPK_SCORE 67 67 12.9256 . . ID=CENPK_all_peaks;Name=chrI67;PEAK=peak0;Note=score
> > is 12.9256
> > chrI SNPScanner
> > CENPK_SCORE 68 68 13.195 . . ID=CENPK_all_peaks;Name=chrI68;PEAK=peak0;Note=score
> > is 13.195
> > chrI SNPScanner
> > CENPK_SCORE 69 69 22.7127 . . ID=CENPK_all_peaks;Name=chrI69;PEAK=peak0;Note=score
> > is 22.7127
> > chrI SNPScanner
> > CENPK_SCORE 70 70 23.8289 . . ID=CENPK_all_peaks;Name=chrI70;PEAK=peak0;Note=score
> > is 23.8289
> > chrI SNPScanner
> > CENPK_SCORE 71 71 21.9123 . . ID=CENPK_all_peaks;Name=chrI71;PEAK=peak0;Note=score
> > is 21.9123
> > chrI SNPScanner
> > CENPK_SCORE 72 72 28.3344 . . ID=CENPK_all_peaks;Name=chrI72;PEAK=peak0;Note=score
> > is 28.3344
> > chrI SNPScanner
> > CENPK_SCORE 73 73 35.0436 . . ID=CENPK_all_peaks;Name=chrI73;PEAK=peak0;Note=score
> > is 35.0436
> > chrI SNPScanner
> > CENPK_SCORE 74 74 37.361 . . ID=CENPK_all_peaks;Name=chrI74;PEAK=peak0;Note=score
> > is 37.361
> > chrI SNPScanner
> > CENPK_SCORE 75 75 39.5408 . . ID=CENPK_all_peaks;Name=chrI75;PEAK=peak0;Note=score
> > is 39.5408
> > chrI SNPScanner
> > CENPK_SCORE 76 76 28.2008 . . ID=CENPK_all_peaks;Name=chrI76;PEAK=peak0;Note=score
> > is 28.2008
> > chrI SNPScanner
> > CENPK_SCORE 77 77 32.6254 . . ID=CENPK_all_peaks;Name=chrI77;PEAK=peak0;Note=score
> > is 32.6254
> > chrI SNPScanner
> > CENPK_SCORE 78 78 36.0832 . . ID=CENPK_all_peaks;Name=chrI78;PEAK=peak0;Note=score
> > is 36.0832
> > chrI SNPScanner
> > CENPK_SCORE 79 79 41.9883 . . ID=CENPK_all_peaks;Name=chrI79;PEAK=peak0;Note=score
> > is 41.9883
> > chrI SNPScanner
> > CENPK_SCORE 80 80 32.1205 . . ID=CENPK_all_peaks;Name=chrI80;PEAK=peak0;Note=score
> > is 32.1205
> > chrI SNPScanner
> > CENPK_SCORE 81 81 41.3048 . . ID=CENPK_all_peaks;Name=chrI81;PEAK=peak0;Note=score
> > is 41.3048
> > chrI SNPScanner
> > CENPK_SCORE 82 82 30.7975 . . ID=CENPK_all_peaks;Name=chrI82;PEAK=peak0;Note=score
> > is 30.7975
> > chrI SNPScanner
> > CENPK_SCORE 83 83 29.4282 . . ID=CENPK_all_peaks;Name=chrI83;PEAK=peak0;Note=score
> > is 29.4282
> > chrI SNPScanner
> > CENPK_SCORE 84 84 35.3586 . . ID=CENPK_all_peaks;Name=chrI84;PEAK=peak0;Note=score
> > is 35.3586
> > chrI SNPScanner
> > CENPK_SCORE 85 85 34.1426 . . ID=CENPK_all_peaks;Name=chrI85;PEAK=peak0;Note=score
> > is 34.1426
> > chrI SNPScanner
> > CENPK_SCORE 86 86 30.2966 . . ID=CENPK_all_peaks;Name=chrI86;PEAK=peak0;Note=score
> > is 30.2966
> > chrI SNPScanner
> > CENPK_SCORE 87 87 17.8402 . . ID=CENPK_all_peaks;Name=chrI87;PEAK=peak0;Note=score
> > is 17.8402
> > chrI SNPScanner
> > CENPK_SCORE 88 88 15.2637 . . ID=CENPK_all_peaks;Name=chrI88;PEAK=peak0;Note=score
> > is 15.2637
> > chrI SNPScanner
> > CENPK_SCORE 89 89 12.657 . . ID=CENPK_all_peaks;Name=chrI89;PEAK=peak0;Note=score
> > is 12.657
> > chrI SNPScanner
> > CENPK_SCORE 90 90 10.2033 . . ID=CENPK_all_peaks;Name=chrI90;PEAK=peak0;Note=score
> > is 10.2033
> > chrI SNPScanner
> > CENPK_SCORE 91 91 9.40143 . . ID=CENPK_all_peaks;Name=chrI91;PEAK=peak0;Note=score
> > is 9.40143
> > chrI SNPScanner
> > CENPK_SCORE 92 92 6.56273 . . ID=CENPK_all_peaks;Name=chrI92;PEAK=peak0;Note=score
> > is 6.56273
> > chrI SNPScanner
> > CENPK_SCORE 93 93 3.66211 . . ID=CENPK_all_peaks;Name=chrI93;PEAK=peak0;Note=score
> > is 3.66211
> > chrI SNPScanner
> > CENPK_SCORE 94 94 0.394194 . . ID=CENPK_all_peaks;Name=chrI94;PEAK=peak0;Note=score
> > is 0.394194
> >
> > CONFIG:
> >
> >
> > GRAPH_CENPK{CENPK_SCORE/CENPK_GRAPH}
> >
> > [CENPK_all_scores_graph]
> > feature = GRAPH_CENPK:SNPScanner
> > glyph = xyplot
> > graph_type = boxes
> > fgcolor = purple
> > bgcolor = purple
> > height = 100
> > min_score = 0
> > max_score = 110
> > label = 0
> > key = CENPK prediction signal
> > link =
> > category = SNPs: signal graphs
> >
> >
> >
> > -------------------------------------------------------------------------
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> >
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse at lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
> >
> >
>
>
> --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT michelse at cshl.edu
>

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu