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

[Tamas Nepusz]

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
>>>
>>>
>>>
>>> _______________________________________________
>>> igraph-help mailing list
>>> address@hidden
>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>
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