Hi Tamas, Thanks a lot for your reply. This sounds like a y complicated solution of the problem. I'm saying this because before I would just vary one parameter and get the result I wanted, whereas now I'd need to design an entire function to merge the connected components. Is there a simple way of doing that? Would you be willing to give a simple exaple? The one on the help page doesn't seem to do what I need.
Thanks a lot, R > On 5 Mar 2016, at 20:48, Tamas Nepusz <[email protected]> wrote: > > 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 > <[email protected]> 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: [email protected] >> twitter: @RafalMostowy >> website: http://rmostowy.wordpress.com >> >> >> >> _______________________________________________ >> igraph-help mailing list >> [email protected] >> https://lists.nongnu.org/mailman/listinfo/igraph-help > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
