[Bioc-devel] Classes to be supported by ggraph

Robert Castelo robert.castelo at upf.edu
Sun Feb 7 23:09:48 CET 2016


i use the part of the functionality of the graph package within my 
packages qpgraph and VariantFiltering. I mostly use the 'graphBAM' class 
that provides a memory-efficient representation of the graph and the 
possiblity to store data associated with nodes and edges via the 
'nodeData()' and 'edgeData()' setters and getters.

while the graph package is not among the most actively developed one, it 
may have about 80 other packages that depend or import its 
functionality. i guess there are ways to explore automatically what 
functionality is used or just what is more popular, which can give you a 
hint about what to implement in 'ggraph'.



On 2/6/16 12:20 PM, Thomas Lin Pedersen 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
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