[Bioperl-l] Heat map module ?

Jason Stajich jason at bioperl.org
Mon Jan 12 15:28:54 UTC 2009

Personally I'd not try and run R within RSPerl or the like so much as  

1) write my data file out in a nice table (to a tempdir)
2) write out a file with the series of R commands you need to make the  
heatmap (with full path to the datafile)
  have the script generate a PNG
3) run the command `R --no-save < tempdir/tempscript.R
4) return the PNG as the result from the cgi and/or tempfile and/or  
using a CGI session
5) cleanup the tempdir and depending on what you do, tag the png file  
for cleanup after a certain time.

On Jan 12, 2009, at 3:49 PM, K. Shameer wrote:

> Hi Jason,
> Thanks for your suggestions.
> I tried Statistics::R, but failed to install it properly. I need to
> generate these plots on-the-fly with in a web server, thats why I  
> prefer
> to do it using Perl than R.
> Thanks for the pointer towards 'heat_map' glyph. I am looking for
> something similar to this, but not in a genome/gbrowse context. For
> example, I have 25*3 matrix with some values. I need to plot it  
> based on a
> gray scale heat map.
> K. Shameer
>> Seems like R is a better place for this - there are heatmap modules  
>> in
>> there.
>> Otherwise GD is what you want for plotting.
>> There is a heat_map-type rendering glyph in Gbrowse if you want to  
>> see
>> this type of stuff across the genome.
>> -jason
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Jason Stajich
jason at bioperl.org

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