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]] >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ >> 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