Re: [igraph] layout repeatability in R ?

[Olivier Delrieu]

Dear Gábor,

Many thanks - This is extremely useful.

I'll make a point in citing igraph when we will publish our work.

Cheers,

Olivier.

Gábor Csárdi wrote:
> Dear Olivier,
>
> On Wed, Apr 21, 2010 at 10:49 PM, Olivier Delrieu <address@hidden> wrote:
>   
>> Dear All,
>>
>> I am wondering how to achieve layout repeatability with igraph in R,
>> especially with the Kamada-Kawai and Fruchterman-Reingold algorithms? By
>> this I mean ability to produce the same result given fully specified
>> starting conditions.
>>     
>
> I agree that repeatability is nice in general. But in this case, can't
> you just simply save the calculated coordinates and pass them along,
> together with the graph?
>
> Anyway, you can get the same results, just set the seed of the random
> number generator:
>
> library(igraph)
> g <- graph.de.bruijn(5,2)
>
> set.seed(123)
> coord <- layout.kamada.kawai(g)
>
> set.seed(123)
> coord2 <- layout.kamada.kawai(g)
>
> max(abs(coord - coord2))
>
>   
>> This is quite important when exchanging data & results with other
>> researchers. Also, Kamada-Kawai can be used for quickly generating an
>> advantageous initial layout which can be passed to Fruchterman-Reingold
>> for a visually more significant placement of neighbored nodes.
>>
>> The code below shows this is not the case with layout.drl despite
>> providing seed coordinates to the algorithm. Am I missing something?
>>     
>
> I think this just shows that the DrL algorithm is stochastic. Plus,
> even if started from the same initial positions, you get different
> results.
>
>   
>> Regarding Kamada-Kawai, and Fruchterman-Reingold the C++ code shows
>> initial configuration can be provided with 'use_seed' and 'res', but
>> these parameters are not documented in the R equivalent. See:
>> http://igraph.sourceforge.net/doc/html/igraph_layout_kamada_kawai.html
>> http://igraph.sourceforge.net/doc/html/igraph_layout_fruchterman_reingold.html
>> http://igraph.sourceforge.net/doc/R/layout.html
>>     
>
> Indeed, I'll fix this.
>
> Best,
> Gabor
>
>   
>> R code:
>>
>> library(igraph)
>> g <- graph.de.bruijn(5,2)
>> coord <- layout.kamada.kawai(g)
>> coord2 <- layout.drl(g, use.seed=TRUE, seed=coord)
>> coord3 <- layout.drl(g, use.seed=TRUE, seed=coord)
>> X11()
>> plot(g,layout=coord2)
>> X11()
>> plot(g,layout=coord3)
>>
>>
>> Many thanks,
>>
>> Olivier.
>>
>>
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>>
>>     
>
>
>
>