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You could also construct the plot directly using the <a href="http://cran.r-project.org/web/packages/network/index.html" rel="nofollow noreferrer">network</a> package, which I think ggnet is using under the hood. <pre><code># Dominik's data structure edgelist<-structure(c(2L, 6L, 2L, 6L, 7L, 7L, 2L, 7L, 6L, 8L, 8L, 4L, 8L, 2L, 9L, 8L, 7L, 6L, 9L, 1L, 9L, 4L, 9L, 3L, 2L, 10L, 9L, 10L, 8L, 10L, 7L, 6L, 10L, 1L, 2L, 12L, 9L, 8L, 12L, 1L, 11L, 10L, 2L, 44L, 79L, 10L, 8L, 47L, 45L, 51L, 9L, 11L, 74L, 75L, 77L, 69L, 75L, 77L, 78L, 2L, 44L, 44L, 46L, 46L, 8L, 6L, 1L, 1L, 6L, 7L, 1L, 4L, 7L, 8L, 8L, 1L, 4L, 8L, 3L, 8L, 8L, 9L, 9L, 9L, 1L, 9L, 5L, 9L, 3L, 9L, 9L, 9L, 10L, 8L, 10L, 7L, 10L, 10L, 1L, 10L, 10L, 9L, 12L, 12L, 1L, 12L, 12L, 12L, 12L, 7L, 7L, 44L, 44L, 44L, 44L, 44L, 44L, 44L, 44L, 44L, 44L, 7L, 7L, 7L, 7L, 44L, 10L, 9L, 42L, 43L, 46L, 46L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, -1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, -1L, 1L, 1L, 1L, -1L, -1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, -1L), .Dim = c(66L, 3L), .Dimnames = list(NULL, c("from", "to", "impact"))) # construct a network object net<-as.network.matrix(edgelist,matrix.type='edgelist', ignore.eval=FALSE,names.eval='impact') # plot it, using the impact edge attribute to control edge color plot(net,edge.col=ifelse(net%e%'impact'==1,'green','red')) </code></pre> <img src="https://i.stack.imgur.com/wvyPi.jpg" alt="enter image description here"> Nate Pope's answer above about changing the range of the ids to remove isolates still applies. However, you can ask plot.network not to draw the isolates: <pre><code>plot(net,edge.col=ifelse(net%e%'impact'==1,'green','red'),displayisolates=FALSE) </code></pre> <img src="https://i.stack.imgur.com/hMJ6V.jpg" alt="enter image description here">
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1. POSet color for segments in ggnet
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1. USskyebend
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