igraph: Resolving tight overlapping nodes

Question

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?

mindlessgreen · Accepted Answer · 2022-04-25T13:39:20.530

I managed to get it to work using package qgraph.

Here is a working example:

library(igraph)
#> 
#> Attaching package: 'igraph'
#> The following objects are masked from 'package:stats':
#> 
#>     decompose, spectrum
#> The following object is masked from 'package:base':
#> 
#>     union
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,names=FALSE)
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()

^{Created on 2022-04-25 by the reprex package (v2.0.1)}

Session info

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@mf In you code the 'e <- get.edgelist(g)' needs to contain index. Then, you need change for 'e <- get.edgelist(g,names=False)' — fmassica, Jul 13 '17 at 14:05
@fmassica This worked for me, but `False` produces an error. The correct syntax is either `F` or `FALSE`. — timothyjgraham, Aug 07 '18 at 01:54
For me it started crashing when not using @fmassica's `names=false`. Without the argument it first gave me a character matrix. When I manually transformed the characters to numeric, it crashed at the stage of plotting. Glad I saw the comment :-) — Simon Stolz, Feb 01 '21 at 17:05

igraph: Resolving tight overlapping nodes

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