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

[Mostowy, Rafal J]

Thanks, this sounds insanely complicated. I don’t understand why someone would 
discontinue such a useful parameter, it’s not very user-friendly. 

Would you be so kind and point me to the right functions which I should use for 
a) finding centre of mass
b) scaling
? I could probably find the solution myself but then I’d spend a whole day on 
this.

Thanks,
R


> On 9 Mar 2016, at 10:44, Tamas Nepusz <address@hidden> wrote:
> 
> Hello,
> 
> Ah, okay - I might have misunderstood your original question (for some
> reason I was thinking that the original problem was that the connected
> components diverged in the layout from each other, resulting in an
> unusable layout).
> 
> I'm afraid that there is no way to control the distance between the
> individual connected components in a layout generated by igraph right
> now. I would probably tackle the problem by post-processing the layout
> a bit:
> 
> 1) Identify the center of mass for each of the connected components in
> the layout
> 2) Scale the vertices of each connected component around the center of
> mass of the component with a scaling factor. (Factors larger than 1
> will make the components get closer to each other, while factors
> smaller than 1 will increase the distance between the components).
> 
> I know that this is a bit cumbersome, but I cannot think of any easier
> solution right now.
> 
> T.
> 
> 
> On Mon, Mar 7, 2016 at 6:04 PM, Mostowy, Rafal J
> <address@hidden> wrote:
>> 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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