[BioRuby] addition of graphics classes

[jan aerts (RI)]

Hi all,

I've been hacking away to create two classes that allow for visualizing
mapping data:
------------------------
Bio::Map::ComparativeMap
------------------------
The first class Bio::Map::ComparativeMap makes it possible to show the
relationship between different maps that have markers in common. As a
result, different maps for the same chromosome (e.g. two different
linkage maps and a radiation hybrid map) can be compared easily. A usage
example is available in the documentation (see attachment
graphics_docs.tar.gz).

The SVG of this particular example looks like the one in the attached
screencast (screencast_comparative_map.html). As the display can get
cluttered if more than 2 maps have to be displayed and there are common
markers between any two maps, some javascript is used to make the maps
draggable by the user.

-------------
Bio::Graphics
-------------
In addition to the Bio::Map::ComparativeMap above, I've created a class
to visualize features on a map, akin to BioPerl's Bio::Graphics module.
It basically works by creating a panel that contains tracks with
features. At the moment, features can be drawn as boxes, directed-boxes
or triangles. An example is added in attachment (output.png; mind that
the quality went way down when converting from the original SVG). At the
moment, the following classes exist:
  Bio::Graphics::Panel
  Bio::Graphics::Panel::Scale
  Bio::Graphics::Panel::Track
  Bio::Graphics::Panel::Track::Feature

Visualizing anything else than features on a linear map is not available
(yet?).

My questions are:
* Would you like me to commit them to bioruby?
* If so: what about naming. Any better suggestions than the two above? I
might move ComparativeMap to Bio::Graphics, as it does nothing more than
drawing things (Bio::Graphics::ComparativeMap?).

Documentation for both modules is also attached (graphics_docs.tar.gz).


Sorry for all those attachments... If you have problems opening any of
them, please let me know.

Looking forward to your comments.


Dr Jan Aerts
Bioinformatics Group
Roslin Institute
Roslin, Scotland, UK
+44 131 527 4200

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