[BioRuby] addition of graphics classes
jan aerts (RI)
jan.aerts at bbsrc.ac.uk
Wed Nov 22 15:43:20 UTC 2006
I've been hacking away to create two classes that allow for visualizing
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
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
draggable by the user.
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:
Visualizing anything else than features on a linear map is not available
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
Roslin, Scotland, UK
+44 131 527 4200
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