[Gmod-help] GBrowse2: imagemaps and scales on xyplot tracks

[Scott Cain]

Hi Jonathan,

Several things:

1. It is best to ask questions like this on the GBrowse mailing list:

  https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

2. The xyplot glyph is only for plotting a single series of data, so you
would want to use two tracks for two separate series (like male and female).

3. The reason you are getting a y axis for each point is that the data
aren't properly "grouped" so that GBrowse knows they go together.  Please
see the tutorial section that deals with the xyplot glyph:

  http://localhost/gbrowse/tutorial/tutorial.html#graph

or

  http://localhost/gbrowse2/tutorial/tutorial.html#graph

Scott


On Fri, Mar 5, 2010 at 12:32 PM, Jonathan Arvisais <
Jonathan.Arvisais at dnalandmarks.ca> wrote:

>
> Hi,
>
> We have features displayed on a xyplot track. When two features have the
> same position, it's impossible for users to see the details (link and
> balloon hover) of one of those features because their link/hover rectangles
> on the imagemap entirely overlap each other.
>
> For example, these two features:
> chr        lineA        association        4719228        4719228
>  1.716993287        .        .
>  Name=Male_feature_123;ID=10987;Ptype=0.05;Datatype=Male;P_value=0.020
> chr        lineA        association        4719228        4719228
>  2.716472047        .        .
>  Name=Female_feature_123;ID=65432;Ptype=0.01;Datatype=Female;P_value=0.003
>
> This is how the features are displayed on our track
> (gbrowse2_1-features.gif):
>
>
> This is the rectangle on the imagemap that shows the balloon on mouse hover
> and that links to both features' link (it's actually 2 pixels wide, but I
> drew it 3 pixels wide for better visibility). It covers the whole height of
> the track, but only 2 pixels wide even though the glyph's radius is 5 pixels
> (gbrowse2_2-actual-imagemap.gif):
>
>
> I think it would be better if the imagemap's rectangles actually fit the
> glyphs' height and width like this (gbrowse2_3-right-imagemap-female.gif and
> gbrowse2_4-right-imagemap-male.gif):
>
>
>
> Also, the scales are repeated for each feature, which can mess up the
> display of a track (gbrowse2_5-actual-scale-repeated.gif):
>
>
> Could it be possible to have scale settings like leftmargin, rightmargin,
> bothmargin in addition to none, left, right, and both?
> (gbrowse2_6-actual-scale-repeated.gif and gbrowse2_7-scale-leftmargin.gif):
>
>
> For example, I did a quick fix by adding #JA lines in
> Bio::Graphics::Glyph::xyplot::_draw_scale() and it does show only one scale
> in the left margin:
> my $x0 = 20;    #JA (should get some value from GBrowse's margin settings)
> ...
> $gd->line($x0,$y1,$x0,$y2,$fg) if $side eq 'leftmargin';    #JA
> ...
> for (sort {$a->[0]<=>$b->[0]} @points) {
>     ...
>     $gd->line($x0-3,$_->[0],$x0,$_->[0],$fg) if $side eq 'leftmargin';
>  #JA
>     ...
>     if ($side eq 'leftmargin') {    #JA
>       $gd->string($font,    #JA
>           $x0 - $font->width * length($_->[1]) - 3,$font_pos,    #JA
>           $_->[1],    #JA
>           $fg);    #JA
>     }
>     ...
> }
>
>
> Thanks!
>
> *_______* *
> Jonathan Arvisais*
> Programmeur Informatique
>
> T: (450) 358-2621 x224
> DNA Landmarks Inc.
> 84 Richelieu
> St.-Jean-sur-Richelieu, J3B 6X3
> Québec, Canada *
> **arvisaisj at dnalandmarks.ca* <arvisaisj at dnalandmarks.ca>*
> **www.dnalandmarks.ca* <http://www.dnalandmarks.ca/>
>
> *DNA LandMarks* *
> une compagnie de* BASF Plant Science *
> a* BASF Plant Science *company*
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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