Does anyone know of any existing R (r-project) code/library/package for drawing graphs - the network variety consisting of nodes and edges (or points and lines/arrows)? e.g. Genes and interactions For example, I might have a list of three edges for four genes: Gene1 -> Gene2 Gene2 -> Gene3 Gene4 -> Gene3 Which would give the following simple graph: Gene1 -> Gene2 -> Gene3 <- Gene4 Or perhaps as a matrix, which for four genes would be 4 by 4: [ 0 1 0 0 ] [ 0 0 1 0 ] [ 0 0 0 0 ] [ 0 0 1 0 ] Here I have used the "rows" as the "from" and the columns as the "to" connections. I was hoping there was an existing library that would accept this sort of network definition and draw a picture of it. Maybe labelled circles for the nodes (genes) with arrows for the edges (interactions). The hard part of this is the spatial layout of the nodes to avoid the edges intersecting unrelated nodes. One simple answer is to draw the nodes equally spaces on a large circle. Apart from the special case of self interactions, all the edges would be inside the circle and thus never cross another node. e.g. This sort of image: http://www.cs.toronto.edu/~wayne/research/ramsey/r.3.9.35.gif Of course there is the extra gloss of being able to draw a connection weight using line thickness etc. Any ideas? I haven't found anything on Google... Thank you Peter

Look at Rgraphviz in bioconductor--it does just this. Sean On 2/2/06 10:57 AM, "Peter" <bioconductor-mailinglist at="" maubp.freeserve.co.uk=""> wrote: > Does anyone know of any existing R (r-project) code/library/package for > drawing graphs - the network variety consisting of nodes and edges (or > points and lines/arrows)? > > e.g. Genes and interactions > > For example, I might have a list of three edges for four genes: > > Gene1 -> Gene2 > Gene2 -> Gene3 > Gene4 -> Gene3 > > Which would give the following simple graph: > > Gene1 -> Gene2 -> Gene3 <- Gene4 > > Or perhaps as a matrix, which for four genes would be 4 by 4: > > [ 0 1 0 0 ] > [ 0 0 1 0 ] > [ 0 0 0 0 ] > [ 0 0 1 0 ] > > Here I have used the "rows" as the "from" and the columns as the "to" > connections. > > I was hoping there was an existing library that would accept this sort > of network definition and draw a picture of it. Maybe labelled circles > for the nodes (genes) with arrows for the edges (interactions). > > The hard part of this is the spatial layout of the nodes to avoid the > edges intersecting unrelated nodes. One simple answer is to draw the > nodes equally spaces on a large circle. Apart from the special case of > self interactions, all the edges would be inside the circle and thus > never cross another node. > > e.g. This sort of image: > > http://www.cs.toronto.edu/~wayne/research/ramsey/r.3.9.35.gif > > Of course there is the extra gloss of being able to draw a connection > weight using line thickness etc. > > Any ideas? I haven't found anything on Google... > > Thank you > > Peter > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

Hi Peter, You can try http://graphexploration.cond.org/ which allows interface to R and its cool software with all lines, arrows, nodes etc, and you can do GeneOntology lay out and Query...as well......!! Howmany genes (neurotrnsmitter TAG Domain) --> interacts with --> endocytosis TAG Domain may be better than cytoscape..!! ( not sure ) Saurin -- |------------------------------------------------ | Saurin D. Jani,MS | Statistical and Research Analyst | | Department of Cell Biology and Anatomy | Medical University of South Carolina (MUSC) | 173 Ashley Ave | Charleston,SC - 29407 | | Email: jani at musc.edu | Phone: (843)792-1340 | Website: http://www.musc.edu/~jani |------------------------------------------------ Quoting Peter <bioconductor-mailinglist at="" maubp.freeserve.co.uk="">: > Does anyone know of any existing R (r-project) code/library/package for > drawing graphs - the network variety consisting of nodes and edges (or > points and lines/arrows)? > > e.g. Genes and interactions > > For example, I might have a list of three edges for four genes: > > Gene1 -> Gene2 > Gene2 -> Gene3 > Gene4 -> Gene3 > > Which would give the following simple graph: > > Gene1 -> Gene2 -> Gene3 <- Gene4 > > Or perhaps as a matrix, which for four genes would be 4 by 4: > > [ 0 1 0 0 ] > [ 0 0 1 0 ] > [ 0 0 0 0 ] > [ 0 0 1 0 ] > > Here I have used the "rows" as the "from" and the columns as the "to" > connections. > > I was hoping there was an existing library that would accept this sort > of network definition and draw a picture of it. Maybe labelled circles > for the nodes (genes) with arrows for the edges (interactions). > > The hard part of this is the spatial layout of the nodes to avoid the > edges intersecting unrelated nodes. One simple answer is to draw the > nodes equally spaces on a large circle. Apart from the special case of > self interactions, all the edges would be inside the circle and thus > never cross another node. > > e.g. This sort of image: > > http://www.cs.toronto.edu/~wayne/research/ramsey/r.3.9.35.gif > > Of course there is the extra gloss of being able to draw a connection > weight using line thickness etc. > > Any ideas? I haven't found anything on Google... > > Thank you > > Peter > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >