[igraph] How to optimise layout without 'area' option?

[Mostowy, Rafal J]

I'm trying to optimise the layout of a network I'm constructing with the 
following code:

gr <- read.table("data.txt", header = F, stringsAsFactors = F)
node.names <- gr[,1]
node.names <- toupper(substr(node.names, 2, nchar(node.names)))
gr <- gr[,-1]
edge.table.index <- which(gr>0.5, arr.ind=T)
d <- data.frame(first = node.names[edge.table.index[,1]], second = 
node.names[edge.table.index[,2]]) 
g <- graph.data.frame(d, directed=F)
g[from=V(g), to=V(g)] <- 0
layout.g <- layout.fruchterman.reingold(g)
plot(g, layout = layout.g, vertex.size = 5, vertex.label.cex=.7, vertex.color = 
"lightblue", vertex.label.family = "sans", edge.color="black", 
vertex.frame.color= "white")

In particular, what I'm trying to do is decrease the area on which the nodes 
are displayed such that the connected components are closer together. Previous 
versions of igraph had the option 'area' in the layout.fruchterman.reingold() 
function but this doesn't seem to be the case anymore. I've tried playing with 
various options like vertex size, vertex font size and width/height of the 
exported pdf file but they don't really do the trick.

Does anyone have a suggestion? I’m attaching a link to the data.

Thanks,
Rafal





________________
Rafal Mostowy, PhD
Junior Research Fellow
Department of Infectious Disease Epidemiology
Imperial College London
St Mary's Campus
Norfolk Place
London W2 1PG
email: address@hidden
twitter: @RafalMostowy
website: http://rmostowy.wordpress.com

data.txt
Description: data.txt