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

Thu Dec 14 21:56:41 UTC 2006

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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>

-- 
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