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

[Mostowy, Rafal J]

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 <address@hidden> 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
> <address@hidden> 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 <address@hidden> 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
>>> <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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>>> 
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