Bug #13361 for GO-TermFinder: GO::View shows larger GO trees only partially

Wed Jun 22 03:43:47 2005 Guest - Ticket created

Subject:

GO::View shows larger GO trees only partially

Dear Author, The GO::View module version 0.70 does not display larger GO trees completely. This seems to be due to the maxTopNodeToShow variable declared in View.pm, line 2285. This variable is set to 6, which corresponds to the number of different root go categories (ie have genes attached directly) that are shown in the graph. If this number is higher than 6 (which happened in my case), an incomplete tree is shown and a discrepancy has arisen between the go tree and the printed output of the significant go categories. Changing this variable to an arbitrary high number (eg 1000) resolves this, an alternative is to completely get rid of this variable ( is it there for performance issues ?), or at least give a warning when you exceed this parameter. Kind regards, Patrick

Sun Jun 26 20:48:53 2005 SHERLOCK [...] cpan.org - Correspondence added

Hi Patrick, You're right - it is arbitrary, and can lead to misleading output. I believe it was added originally for performance considerations when running as a cgi, which was the intended use for GO::View when written by the Saccharomyces Genome Database. I think documenting the behavior, and and making it modifiable via a config variable would be reasonable, as well as giving a warning. I'll put it on my list of things for the next release, Cheers, Gavin [guest - Wed Jun 22 03:43:47 2005]: Show quoted text

> Dear Author, > > The GO::View module version 0.70 does not display larger GO trees > completely. This seems to be due to the maxTopNodeToShow variable > declared in View.pm, line 2285. This variable is set to 6, which > corresponds to the number of different root go categories (ie have > genes attached directly) that are shown in the graph. If this > number is higher than 6 (which happened in my case), an incomplete > tree is shown and a discrepancy has arisen between the go tree and > the printed output of the significant go categories. Changing this > variable to an arbitrary high number (eg 1000) resolves this, an > alternative is to completely get rid of this variable ( is it there > for performance issues ?), or at least give a warning when you > exceed this parameter. > > Kind regards, > > Patrick

Mon Jun 27 04:22:06 2005 Guest - Correspondence added

Dear Gavin, Making it a configurable parameter seems a very good idea to me. Thanks for your time so far! Regards, Patrick [SHERLOCK - Sun Jun 26 20:48:53 2005]: Show quoted text

> Hi Patrick, > > You're right - it is arbitrary, and can lead to misleading output. I > believe it was added > originally for performance considerations when running as a cgi, which > was the intended use > for GO::View when written by the Saccharomyces Genome Database. I > think documenting the > behavior, and and making it modifiable via a config variable would be > reasonable, as well as > giving a warning. I'll put it on my list of things for the next > release, > > Cheers, > Gavin > > > [guest - Wed Jun 22 03:43:47 2005]: >

> > Dear Author, > > > > The GO::View module version 0.70 does not display larger GO trees > > completely. This seems to be due to the maxTopNodeToShow variable > > declared in View.pm, line 2285. This variable is set to 6, which > > corresponds to the number of different root go categories (ie

> have

> > genes attached directly) that are shown in the graph. If this > > number is higher than 6 (which happened in my case), an

> incomplete

> > tree is shown and a discrepancy has arisen between the go tree

> and

> > the printed output of the significant go categories. Changing

> this

> > variable to an arbitrary high number (eg 1000) resolves this, an > > alternative is to completely get rid of this variable ( is it

> there

> > for performance issues ?), or at least give a warning when you > > exceed this parameter. > > > > Kind regards, > > > > Patrick

> >