[Bioc-devel] Classes to be supported by ggraph

Wolfgang Huber whuber at embl.de
Sat Feb 6 22:16:31 CET 2016

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

> On Feb 6, 2016, at 12:20 GMT+1, Thomas Lin Pedersen <thomasp85 at 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]]
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Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
Genome Biology Unit
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.huber at embl.de

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