add igraph to d3 converter

[timelyportfolio]

While talking with @ttriche on Twitter, I remembered a helpful function would be to convert igraph to a "standard" d3.js network. I have some preliminary code that will require testing and iteration.

[ttriche]

mine looks something like this (pulling out part of a protein-protein network):

# pull out CREBBP for discussion 
library(networkD3)
toD3 <- function(g) { 
  wc <- cluster_walktrap(g) 
  members <- membership(wc)
  igraph_to_networkD3(g, group=members)
}
plotForceNet <- function(g, ...) {
  stopifnot(is(g, "igraph"))
  with(toD3(g), 
       forceNetwork(Links=links, Nodes=nodes, 
                    Source="source", Target="target", 
                    NodeID="name", Group="group", 
                    zoom=TRUE, bounded=TRUE, ...))
}
CREBBP_sub <- induced_subgraph(mergedGraph, 
                               ego(mergedGraph, 1, 
                                   which(names(V(mergedGraph))=="CREBBP"))[[1]])
p <- plotForceNet(CREBBP_sub, fontSize=12, opacity=0.9, opacityNoHover=0.3)
saveNetwork(p, file="CREBBP.html") # uploaded to amazon S3

[timelyportfolio]

Thanks @ttriche. The networkd3::igraph_to_networkD3 works fairly well, but it makes some assumptions for the benefit of its particular use. I think the proposed code is a little more generic, but I'm not convinced. I have not tested with the member/group, so I will do that now to make sure it handles. After that, my next round of tests will be to plug in the converted to multiple examples.

[timelyportfolio]

Add layout if available to allow igraph layouts to be paired with d3.js. This will make for a very powerful combination supplementing d3.js with the igraph layouts, but interactivity will be tricky. Start with just adding x and y attributes and then go from there.

[timelyportfolio]

added attributes to the return value c200062

[timelyportfolio]

Going to close this for now, since I added d3_igraph, but I will very likely resurrect this especially given @thomasp85 work on tidygraph.