>From my perspective Rgraphviz now has a quite good (cross-platform) access to the Graphviz layout routines. But how to actually use these routines from R is certainly something I think could be vastly improved upon. Right now, Rgraphviz basically has two different interfaces to graph layout and graph rendering - the "really, really old" interface and the "only old" interface. As you may sense I don't have strong feelings about the R interface to Rgraphviz, except that I would be very open to someone improving on it. I don't have the time to do that myself. Basically what I do right now is maintain the C interface, since I have spent so much time hacking on it. But the R interface needs a lot of love. I think it would be a shame to not continue to have access to the Graphviz library from R given that it now works and it is extremely widely used.
For the ggraph package I think it would be worthwhile to also be able to use the layout routines in (R)Graphviz, and I don't see why we would not be able to plug into it. How to display a general graph can get pretty burdensome wrt. arguments. One of the original ideas in Rgraphviz was that a use would be able to put a full R plot (say a scatterplot or histogram) inside each node. Best, Kasper On Sat, Feb 6, 2016 at 4:16 PM, Wolfgang Huber <whu...@embl.de> wrote: > Dear Thomas > > thank you for asking about this. > > The main information in a graphNEL is, of course, the vector of nodes > (character) and a list of edges. That information can for sure go into an > igraph. > > Then there is the slot `renderInfo`, which afaIu is (or can be) used to > control how the graph should be rendered when plotted e.g. on a 2D screen > with Rgraphivz. The last big refactoring seems (according to svn blame) due > to Seth Falcon, Nishant Gopalakrishnan and Florian Hahne in 2010/11. (The > package has been worked on by a variety of of people over the years; e.g. > my own involvement dates back to two bursts in 2004 and 07). > > It is hard to tell how much of the renderInfo functionality is used out > there in the wild, but the fact that its code hasn’t been touched for 5 > years is consistent with assuming that interest in it is limited (otherwise > there tend to be bug reports or requests for more functionality). > > Kapser and Florian are probably lurking on this list and waiting to make > additional comments. > > In summary: I think your proposal is great, and you should go ahead. I > expect the downsides, if any, to be miniscule. > > Hope this helps > Wolfgang > > > > On Feb 6, 2016, at 12:20 GMT+1, Thomas Lin Pedersen <thomas...@gmail.com> > wrote: > > > > I’m in the process of developing ggraph ( > https://github.com/thomasp85/ggraph) - An extensive plotting framework > for graph/tree/network data based on ggplot2. Currently the class support > is focused on igraph and dendrogram, but the idea is to extend it with > support for additional graph representations in R. The easy way to do this > is through conversion to one of the two currently supported classes, but I > would like to hear from the developers and users of especially the graph > package, whether there are any downsides to this approach, i.e. are there > features/information captured by the graphNEL class that would disappear > with conversion to an igraph object. > > > > Also if someone is working with, or developing other graph > representations and would like to see support in ggraph, please let me know… > > > > best > > > > Thomas > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > Wolfgang Huber > Principal Investigator, EMBL Senior Scientist > Genome Biology Unit > European Molecular Biology Laboratory (EMBL) > Heidelberg, Germany > > wolfgang.hu...@embl.de > http://www.huber.embl.de > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel