igraph: Resolving tight overlapping nodes

问题

I have a graph with few hundred nodes and edges. The disconnected subgraphs separate out and resolve well but the nodes within subgraphs overlap and do not resolve well. I have tried several layout algorithms and have also tried changing the relevant parameters within the layout algorithm (ex: iter, kkconst, start.temp etc). But, I am still not able to disperse the tightly clustered nodes. See figure below.

I was hoping to find some parameter to control attraction/repulsion/gravity etc but there seems to be none. The answer and figures from bdemarest in this question does seem to fix exactly this issue. Strangely enough, several seemingly useful parameters have been deprecated in the new version of igraph (coolexp, maxdelta, area, repulserad etc).

Does anyone know of a way to keep the sub graphs well separated while spreading out close nodes well enough that they do not overlap?

回答1:

I managed to get it to work using package qgraph.

Here is a working example:

library(igraph)
library(qgraph)

g <- barabasi.game(355, directed=FALSE)

png("plot1.png", height=6, width=12, units="in", res=250)
par(mfrow=c(1, 3))

plot(g,layout=layout_with_fr,vertex.size=4,vertex.label=NA)
mtext("layout_with_fr", side=1)

e <- get.edgelist(g)
l <- qgraph.layout.fruchtermanreingold(e,vcount=vcount(g))
plot(g,layout=l,vertex.size=4,vertex.label=NA)
mtext("qgraph.layout.fruchtermanreingold default", side=1)

l <- qgraph.layout.fruchtermanreingold(e,vcount=vcount(g),
      area=8*(vcount(g)^2),repulse.rad=(vcount(g)^3.1))
plot(g,layout=l,vertex.size=4,vertex.label=NA)
mtext("qgraph.layout.fruchtermanreingold modified", side=1)

dev.off()

来源：https://stackoverflow.com/questions/39290909/igraph-resolving-tight-overlapping-nodes