Re: Questions related to draw graphy using perl

[Chris Devers]

On Fri, 15 Oct 2004, Li, Aiguo (NIH/NCI) wrote:

> Is it possible to create graphs like this using perl?
> 
> The graph in my mind should look like this and it will be better to 
> use histogram bar for meta p-values.
>  
>  
> ---|
>  --|
>|
>   -|
  
Interesting -- that's not one of the typical data visualization 
techniques that most canned tools (from Perl's GD::Graph to, say, 
Excel's chart abilities) usually provide, as far as I know. :-)

Usually on this list, it's expected that people give an overview of what 
they've tried so far, including modules used and code written. In this 
case though, you're asking an interesting but advanced question, and you 
would probably be better off by taking this to the bioperl list:

  Overview:


  Homepage:


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But that said, if you get no help over there, by all means ask away on 
this list. I'm certainly not trying to drive away interesting questions. 

:-)



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Chris Devers

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Questions related to draw graphy using perl

[Li, Aiguo (NIH/NCI)]

Dear all.
 
I am a new user of Perl with some experience in perl data extraction with
pattern matching, but never did anything with making graphy using perl.  I
need to draw a chromosome copy number graphy and p-values.  The data looks
are as follow:
 
SNP id   physical location   copy number meta p-value   
SNP_A-1507380120264678   1.207953-20
SNP_A-1507487120319466   1.261954-20
SNP_A-1517022120783585   0.957751-20
SNP_A-1511651121478764   0.957812-20
SNP_A-151681817549   2.0043180.722914   
SNP_A-1516270122257923   3.2988680.967391   
SNP_A-1512747122611515   1.419261-14.5074   
SNP_A-1519155123556896   0.740608-14.5074   
SNP_A-1517539124789024   1.202693-14.5074   
SNP_A-1511157124890914   1.222511-14.5074   
 
The physical location should be the place where the p-value and copy number
should be along the vertical line.  The SNP id could be treated as
annotation.  I have some open source code available for drawing a chromosome
with cytobands writing in perl.  The final gool is to put this graph of copy
number beside the chromosome map,  which make me think that it will be
easier using perl to do draw this copy number map.  My questions to you is:
 
Is it possible to create graphy like this using perl?
 
The graphy in my mind should look like this and it will be better to use
histogram bar for meta p-values.
 
 
---|
 --|
   |
  -|
 
Thanks in advance,
 
Aiguo Li