[BioC] RGraphViz: length edges

[prsmra01 at uniroma2.it]

Hi Guido,
I share with you my experience and a chunk of code to better clarify  
the concepts;
after many attempts in trying to draw graphs with defined edge  
lengths, my conclusion was that "dot" is the tool most suitable to do  
this,because more "flexible";
  the others (neato and fdp) are more aimed to draw nice graphs  
instead of graphs with precise edge lengths(the value you put for the  
argument len doesn't affect the final result!); the only way I found  
to do something "close" to what I wanted was this: (note the argument  
"weight" aimed to force the program to take more into account the  
value of len parameter)

  graph G  {

overlap = false;
node [shape=box,style=filled,width=.3, height=.3];

ds1N -- ds1P [len=0.16,weight=15];
ds1P -- ds2P [len=0.12,weight=5];
ds1P -- ds2N [len=0.20,weight=5];
ds1N -- ds2P [len=1.00,weight=18];
ds1N -- ds2N [len=0.89,weight=15];
ds2N -- ds2P [len= 0.48,weight=18];

}
  Hope this can help.

Best,
maria
-- 
Maria Persico, PhD
Applied Bioinformatics Group, Biotec, TU Dresden,
Tatzberg 47-51, 01307 Dresden
maria.persico at biotec.tu-dresden.de
persico.maria at gmail.com
Phone:   +49 (0)351 463 40020
Fax:     +49 (0)351 463 40087

e-mail maria.persico at uniroma2.it


Def. Quota "Hooiveld, Guido" <Guido.Hooiveld at wur.nl>:

> Dear list,
>
> I am new to RGraphViz and currently evaluating it's options. So bare  
> with me regarding this basic question....
>
> Say i have three nodes, A, B and C. How can i plot a graph in which  
> the length of the edges between the nodes are user-defined? Say  
> between A en B the length should be 1, between A and C this should  
> be 2, and between B and C this should be 0.5?
> I found that the argument "len" is able to set the length of the edges,
> http://www.graphviz.org/pub/scm/graphviz2/doc/info/attrs.html#d:len
> (len: Preferred edge length, in inches.)
> Also from the info @ the link:
> len; Edge;, double; 1.0 (neato); 0.3(fdp); fdp, neato only
>
>> From the above I conclude that depending on the lay-out (neato or  
>> fdp) the length of ALL edges in the graph are set to 1 and 0.3  
>> inch, respectively.
>
> But how to vary the length per edge? Or is what i would like to to  
> not possible?
>
> Any feedback is much appreciated!
>
> Guido
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet:   http://nutrigene.4t.com<http://nutrigene.4t.com/>
> email:      guido.hooiveld at wur.nl
>
>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:  
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>



----------------------------------------------------------------
Invito da parte dell'Ateneo:
Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del
tuo aiuto. Dona il  5 x mille all'Universita' di Roma Tor Vergata
codice fiscale: 80213750583 http://5x1000.uniroma2.it