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

[Jonathan Arvisais]

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
www.dnalandmarks.ca 
DNA LandMarks 
une compagnie de BASF Plant Science 
a BASF Plant Science company 
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