[Bioperl-l] Bio::Graphics - several
Alper Yilmaz
alperyilmaz at gmail.com
Mon Jul 14 21:34:26 UTC 2008
Hi,
I have couple questions about Bio::Graphics.
a- even though I played around with start, end, width, length values,
I wasn't able to make a ruler which starts from -1600 and ends at 0
(promoter region). How can I make a ruler, which has negative values
and decreases towards right?
In such a case, what happens to start and end values of the box
glyphs? How can I adjust start and end values of an element located at
1500bp so that it's shown at -100bp, in other words are negative
values taken as is or interpreted as "less than start" ?
b- some of the recognized variables for -link argument are $name, $id, etc.
$name corresponds to -display_name of Bio::SeqFeature::Generic.What
does $id correspond to? I tried to assign value to $id but it was not
successful
-link=> sub {
my $element = shift;
my $id = $element->seq_id;
return 'http://database/address.html?promoter_id=$id';
},
In this statement even if I try to print $id within sub, it does not
print anything.
c- I didn't come accross any scripts or tutorials about including pan
or zoom button (as in GBrowser). How can I add those functionalities
to already available graphics generated by Bio::Graphics ?
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