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

[Tamas Nepusz]

Hi,

The new implementation of the Fruchterman-Reingold layout does not
have the "area" option any more, but you can try using
layout_components() - this will decompose the graph into connected
components first, lay out the connected components separately, and
then merge the layouts.

T.


On Sat, Mar 5, 2016 at 2:56 PM, Mostowy, Rafal J
<address@hidden> wrote:
> 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
>
>
>
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