[BioRuby] Bioruby graphics classes

[jan aerts (RI)]

Hey George,

I worked a bit on some Bio::Graphics code, but it still is quite crude
and could use some thorough testing, but at least it's well-documented
:-) How polished do you need the output to be? The code I have at the
moment creates an SVG using a piece of code as sampled at the bottom of
my mail. The actual output picture (in SVG) is attached as an example
and should be opened in FireFox for the links to work.

The setup for this code is similar to that of BioPerl: you have a panel
for the whole graphic, which contains tracks for each of the different
types of features (e.g. 1 track for SNPs, 1 track for genes, ...). Each
track then contains all features of that type.

Note that this code is _not_ in bioruby and it could use some TLC before
reaching its full potential. Issues that still have to be solved:
* Feature names are not be displayed yet.
* The scale does not 'scale' yet: for a large sequence, you just get a
black bar because the tick marks are so close together.
* The SVG doesn't look as nice as I would like in FireFox (maybe produce
PNG instead of SVG)
* It's not possible yet to display just _part_ of your sequence, as if
you zoomed in.
At least some of these issues can be solved in quite a limited period of
time, but unfortunately I'm really covered in work at the moment...


If you want the code, just drop me a line and I'll send you the
necessary files.

jan.

<BEGIN CODE>
#!/usr/bin/ruby
require 'bio_ext'

#Initialize graphic for a nucleotide sequence of 600 bp
my_panel = BioExt::Graphics::Panel.new(600)

#Create and configure tracks
#(NOTE TO SELF: this should be possible with a method_missing)
track_SNP = my_panel.add_track('SNP')
track_gene = my_panel.add_track('gene')
track_transcript = my_panel.add_track('transcript')

track_SNP.feature_colour = 'red'
track_SNP.feature_glyph = 'triangle'
track_gene.feature_glyph = 'directed_generic'
track_transcript.feature_glyph = 'spliced'
track_transcript.feature_colour = 'green'

# Add data to tracks
DATA.each do |line|
  line.chomp!
  ref, type, name, location, link = line.split(/\s+/)
  if link == ''
    link = nil
  end
  if type == 'SNP'
    track_SNP.add_feature(name, location, link)
  elsif type == 'gene'
    track_gene.add_feature(name, location, link)
  elsif type == 'transcript'
    track_transcript.add_feature(name, location, link)
  end
end

# And print out
output = File.new('output.svg', 'w')
output.puts my_panel.to_svg
output.close

__END__
chr1  gene        CYP2D6      50..134
http://www.bioruby.org
chr1  gene        ALDH        250..344
http://www.google.com
chr1  SNP         rs1234      150
http://www.newsforge.com
chr1  gene        bla         complement(400..435)
http://news.bbc.co.uk
chr1  SNP         rs9876      445
http://www.roslin.ac.uk
chr1  gene        some_gene   complement(465..495)
http://digg.com
chr1  transcript  transcript1 join(250..300,390..425)
http://www.ruby-lang.org
chr1  transcript  transcript2 253..330
http://www.sourceforge.net
chr1  transcript  transcript3 266..344

chr1  transcript  transcript4
complement(join(410..430,239..286,129..151)) http://www.vrtnieuws.net 
<END CODE>



> -----Original Message-----
> From: bioruby-bounces at lists.open-bio.org 
> [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of 
> George Githinji
> Sent: 19 April 2007 21:41
> To: bioruby at lists.open-bio.org
> Subject: [BioRuby] Bioruby graphics classes
> 
> Hi everyone!
> Please can someone show me how to access bioruby graphics classes?
> am using bioruby version 1.0.0 but i need to render glyphs 
> for some sequence features
> 
> Thanks
> --
> ---rgds
>   George
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>