Hi Jonathan,<br><br>Several things:<br><br>1. It is best to ask questions like this on the GBrowse mailing list:<br><br> <a href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse">https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</a><br>
<br>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).<br><br>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:<br>
<br> <a href="http://localhost/gbrowse/tutorial/tutorial.html#graph">http://localhost/gbrowse/tutorial/tutorial.html#graph</a><br><br>or<br><br> <a href="http://localhost/gbrowse2/tutorial/tutorial.html#graph">http://localhost/gbrowse2/tutorial/tutorial.html#graph</a><br>
<br>Scott<br><br><br><div class="gmail_quote">On Fri, Mar 5, 2010 at 12:32 PM, Jonathan Arvisais <span dir="ltr"><<a href="mailto:Jonathan.Arvisais@dnalandmarks.ca">Jonathan.Arvisais@dnalandmarks.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br><font face="sans-serif" size="2">Hi,</font>
<br>
<br><font face="sans-serif" size="2">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.</font>
<br>
<br><font face="sans-serif" size="2">For example, these two features:</font>
<br><tt><font size="2">chr lineA
association 4719228
4719228 1.716993287
. .
Name=Male_feature_123;ID=10987;Ptype=0.05;Datatype=Male;P_value=0.020</font></tt>
<br><tt><font size="2">chr lineA
association 4719228
4719228 2.716472047
. .
Name=Female_feature_123;ID=65432;Ptype=0.01;Datatype=Female;P_value=0.003<br>
</font></tt>
<br><font face="sans-serif" size="2">This is how the features are displayed
on our track (gbrowse2_1-features.gif):</font>
<br><img src="cid:_1_04B5FA3C04B5F79C005FE553852576DD"><font face="sans-serif" size="2"> </font>
<br>
<br><font face="sans-serif" size="2">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):</font>
<br><img src="cid:_1_04B611FC04B60AC4005FE553852576DD">
<br>
<br><font face="sans-serif" size="2">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):</font>
<br><img src="cid:_1_04C69CEC04B61064005FE553852576DD"><font face="sans-serif" size="2">
</font><img src="cid:_1_04C69EF004B61064005FE553852576DD">
<br>
<br>
<br><font face="sans-serif" size="2">Also, the scales are repeated for each
feature, which can mess up the display of a track (gbrowse2_5-actual-scale-repeated.gif):</font>
<br><img src="cid:_1_04C6AA0C04C6A7E4005FE553852576DD">
<br>
<br><font face="sans-serif" size="2">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):</font>
<br><img src="cid:_1_04C6AF1804B5EE3C005FE553852576DD"><font face="sans-serif" size="2">
</font><img src="cid:_1_04C6B11C04B5EE3C005FE553852576DD">
<br>
<br><font face="sans-serif" size="2">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:</font>
<br><tt><font size="2">my $x0 = 20; #JA (should get some value
from GBrowse's margin settings)</font></tt>
<br><tt><font size="2">...</font></tt>
<br><tt><font size="2">$gd->line($x0,$y1,$x0,$y2,$fg) if $side eq 'leftmargin';
#JA</font></tt>
<br><tt><font size="2">...</font></tt>
<br><tt><font size="2">for (sort {$a->[0]<=>$b->[0]} @points)
{</font></tt>
<br><tt><font size="2"> ...</font></tt>
<br><tt><font size="2"> $gd->line($x0-3,$_->[0],$x0,$_->[0],$fg)
if $side eq 'leftmargin'; #JA</font></tt>
<br><tt><font size="2"> ...</font></tt>
<br><tt><font size="2"> if ($side eq 'leftmargin') {
#JA</font></tt>
<br><tt><font size="2"> $gd->string($font,
#JA</font></tt>
<br><tt><font size="2"> $x0 - $font->width
* length($_->[1]) - 3,$font_pos, #JA</font></tt>
<br><tt><font size="2"> $_->[1],
#JA</font></tt>
<br><tt><font size="2"> $fg); #JA</font></tt>
<br><tt><font size="2"> }</font></tt>
<br><tt><font size="2"> ...</font></tt>
<br><tt><font size="2">}</font></tt>
<br>
<br>
<br><font face="sans-serif" size="2">Thanks!</font>
<br>
<br><font size="2"><b>_______</b> <b><br>
Jonathan Arvisais</b> <br>
Programmeur Informatique</font>
<p><font size="2">T: (450) 358-2621 x224 <br>
DNA Landmarks Inc. <br>
84 Richelieu <br>
St.-Jean-sur-Richelieu, J3B 6X3<br>
Québec, Canada </font><font color="blue" size="2"><u><br>
</u></font><a href="mailto:arvisaisj@dnalandmarks.ca" target="_blank"><font color="blue" size="2"><u>arvisaisj@dnalandmarks.ca</u></font></a><font color="blue" size="2"><u><br>
</u></font><a href="http://www.dnalandmarks.ca/" target="_blank"><font color="blue" size="2"><u>www.dnalandmarks.ca</u></font></a><font size="2">
</font>
</p><p><font face="Arial" size="2"><b>DNA LandMarks</b></font><font size="2"> </font><font face="Arial" size="1"><i><br>
une compagnie de</i> </font><font face="Arial Black" size="1">BASF Plant
Science </font><font face="Arial" size="1"><i><br>
a</i> </font><font face="Arial Black" size="1">BASF Plant Science </font><font face="Arial" size="1"><i>company</i></font><font size="2">
</font></p></blockquote></div><br><br clear="all"><br>-- <br>------------------------------------------------------------------------<br>Scott Cain, Ph. D. scott at scottcain dot net<br>
GMOD Coordinator (<a href="http://gmod.org/">http://gmod.org/</a>) 216-392-3087<br>Ontario Institute for Cancer Research<br>