Bioperl: libgd and bioperl

[Simon Twigger]

Andreas,

As an alternative, you might want to have a look at PostScript. I have a
PostScript module based loosely on the GD module which makes the
creation of PostScript images about as painless as making gifs using
GD.pm. The trick then is to display them on the browser - I've had a
great deal of success piping the postscript output to Ghostscript to
create a PDF on the fly. This has a number of advantages - it prints
respectably, its searchable, you can do multipage documents, add in
hyperlinks etc. We recently used this to generate the genetic
map/radiation hybrid maps of the rat for both publication and on-line
use (publication quality GIFs arent something you see too often)

Steen etal. Genome Research, May 1999,
http://goliath.ifrc.mcw.edu/LGR/research/rhp/steen_1999.html

The nice thing about the PDF output is that you can open it in
Macromedia Freehand/ Adobe illustrator,etc. and move the graphic
elements around as required, change fonts, edit the lines, etc. Its very
handy if you want to tweak a figure after its been generated. Of course,
being postscript it will scale and stretch up and down and still print
out to the best of your printers ability. If postscript/PDF arent what
you need, You could always take the Postscript and convert it to another
image format using any of the common image processing tools available.

The module itself is called PostScript::Basic. Its listed at CPAN with a
link to the documentation and downloads here:

http://legba.ifrc.mcw.edu/~simont/pub/ps.html

If you give the module a try, please let me know how you get on. Its
still being developed so all advice and suggestions are welcome!

Cheers,

	Simon.


Andreas Matern wrote:
> 
> As mentioned on SlashDot (http://slashdot.org) today, the gd library
> (http://www.boutell.com/gd/) which creates GIFs on the fly and is required
> by Lincoln's GD (http://stein.cshl.org/WWW/software/GD/GD.html) module
> (which I use, in part, for Alessandro Guffanti's Paintblast
> (http://hercules.tigem.it/Biomodules.html) module) has been withdrawn due to
> copyright problems!
> 
> Thought you would like to know....... and maybe ask about graphics and
> bioperl.  The software users I interact with always require graphical
> displays to analyze data -- which is understandable, but makes my life a bit
> difficult.  :-)
> 
> Has the bioperl community tackled many/any graphics issues?  i.e. graphical
> display of chromosomes, BLAST results, contig information, chromatographs,
> etc....


--------------------------------------------------
Simon Twigger, Ph.D.
Laboratory for Genetic Research,
Cardiovascular Research Center,
Medical College of Wisconsin,
8701 Watertown Plank Road, 
Milwaukee, WI, 53226

http://legba.ifrc.mcw.edu/~simont/

tel. 414-456-4409               fax. 414-456-6516
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