[BioC] RGraphViz: length edges

Mon May 31 11:03:10 CEST 2010

Hi,

for me it was important to have the edge lenght  ds1P -- ds2P as the  
smallest on but if you try this you can see that it doesn't work!

#command line
cat test.dot | neato -Teps >out.neatobis.eps
cat test.dot | dot -Teps >out.dotbis.eps
#the input script:
graph G  {

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

ds1N -- ds1P [len=0.16,weight=5];
ds1P -- ds2P [len=0.12,weight=5];
ds1P -- ds2N [len=0.20,weight=4];
ds1N -- ds2P [len=1.00,weight=5];
ds1N -- ds2N [len=0.89,weight=5];
ds2N -- ds2P [len= 0.48,weight=4];

}

Cheers,
Maria
-- 
Maria Persico, PhD. student
http://cbm.bio.uniroma2.it/~maria/
MINT database group
Universita' di Tor Vergata, via della Ricerca scientifica 11
00133 Roma, Italy
Tel +39 0672594315 (Supervisor's room)
Fax +39 0672594766
Mobile phone: +393479715662
e-mail maria.persico at uniroma2.it

Quoting "Michael Lawrence" <lawrence.michael at gene.com>:

> It's my understanding that neato is an implementation of Kamada-Kwai, which
> is going to try to match the distance between two nodes in the
> two-dimensional drawing to a pre-defined distance between nodes. By default,
> I think this distance is defined as the length of the shortest path between
> two nodes, but I'm pretty sure it can be overridden.
>
> I would say that "dot", as a Sugiyama layout, is just going to try to keep
> edge lengths short. Sometimes, due to the constraints of the layout, edges
> can be quite long. I'm a little surprised that 'len' works with dot, since
> the documentation appears to say otherwise.
>
> Michael
>
> On Sun, May 30, 2010 at 3:00 PM, <prsmra01 at uniroma2.it> wrote:
>
>> 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]]
>>>
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>>>
>>>
>>
>>
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>

----------------------------------------------------------------
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