Thanks. I understand the basic concept (though yes, the example you sent is helpful. however I still don’t understand how to control the spread between the connected components. Previously, the area function affected the area across which they’re spread but now I don’t see the appropriate variable. Is there an analogous parameter in the layout_components() function?
> On 7 Mar 2016, at 12:31, Tamas Nepusz <[email protected]> wrote: > > Hi, > > You don't need any function for merging the layouts; > layout_components() will do this for you: > >> library(igraph) >> g <- make_ring(5) * 4 >> layout <- layout_components(g, layout=layout_with_fr) >> plot(g, layout=layout) > > Basically, layout_components will decompose the graph into its > connected components, then call the given layout function > (layout_with_fr in the above example) for all the components, merges > the layouts, and returns a single unified layout that is suitable for > the original graph. Any additional arguments supplied to > layout_components() are forwarded to the actual component-wise layout > function. > > All the best, > T. > > > On Mon, Mar 7, 2016 at 1:20 PM, Mostowy, Rafal J > <[email protected]> wrote: >> 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 > > _______________________________________________ > 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
