Re: [igraph] vertex overlap layout

[Bruno Contreras Moreira]

Here's the code:

1) reading the graph and layout:

net = read.graph(file="net.ncol",format="ncol",direct=T)
clayout = as.matrix(read.table("circle_layout_coords.txt"))

2.1) plot with RESCALE=FALSE:

splot(net,layout=clayout,edge.arrow.size=0.1,rescale=FALSE,xlim=c(1,500),ylim=c(1,400))

2.1) plot with RESCALE=TRUE:

plot(net,layout=clayout,edge.arrow.size=0.1)

In both my linux and XP enviroments, I get the same problem described in 
the previous email, can you give any hint?
Bruno



> No, edges are never "hidden", and I also don't understand what you
> mean by vertices losing their frames. Please send some code that
> reproduces these errors.
>
> Gabor
>
> On Wed, Mar 4, 2009 at 1:33 PM, Bruno Contreras Moreira
> <address@hidden> wrote:
>   
> > OK,
> > I have finally managed to plot a graph with a predefined layout, without
> > vertex overlap. Thanks for your help.
> > However, there is one more problem.
> > If the plot is generated with RESCALE=TRUE, I get a scaled layout with
> > visible vertex frames,
> > but it is not possible to see edges among neighboring vertices, as they get
> > hidden I guess.
> > On the other hand, if I apply RESCALE=FALSE vertices actually loose their
> > frames, regardless of their shape, but I can see all edges.
> > I will like to have both things (all edges and vertex frames), can you
> > suggest a solution for this?
> > Bruno
> >
> >     
> > > Because you have to set 'xlim' and 'ylim' as well, they default to
> > > c(-1,1), I agree that this is quite silly. Anyway, you are zooming in
> > > to an empty region, set 'xlim' and 'ylim'.
> > >
> > > Gabor
> > >
> > > On Tue, Mar 3, 2009 at 2:15 PM, Bruno Contreras Moreira
> > > <address@hidden> wrote:
> > >
> > >       
> > > > Dear Gábor,
> > > > I get an empty plot with rescale=FALSE
> > > >
> > > >
> > > >         
> > > > > Plotting functions rescale the coordinates by default, supply
> > > > > 'rescale=FALSE' to them to avoid this.
> > > > >
> > > > > Gabor
> > > > >
> > > > > On Tue, Mar 3, 2009 at 1:12 PM, Bruno Contreras Moreira
> > > > > <address@hidden> wrote:
> > > > >
> > > > >
> > > > >           
> > > > > > Thanks Gabor,
> > > > > > indeed I had already tried your first suggestion,  ie, exporting the
> > > > > > coordinates from a  tkplot rendering, but although layouts can be
> > > > > > easily
> > > > > > exported as matrices, I haven't been able to correctly export layouts
> > > > > > after
> > > > > > changing the window size. What this means is that if I enlarge a tkplot
> > > > > > circle layout, when I export the coordinates I still get a default size
> > > > > > circle layout, is this a known limitation of igraph?
> > > > > > Best,
> > > > > > Bruno
> > > > > >
> > > > > >
> > > > > >             
> > > > > [...]
> > > > >
> > > > >
> > > > >
> > > > >           
> >
> > _______________________________________________
> > igraph-help mailing list
> > address@hidden
> > http://lists.nongnu.org/mailman/listinfo/igraph-help
> >
> >     
>
>
>
>   


--
Bruno Contreras Moreira
Estación Experimental de Aula Dei /CSIC
Av.Montañana 1.005, 50059 Zaragoza (España).
Tel:(+34) 976716089 Fax:(+34) 976716145
address@hidden http://www.eead.csic.es/compbio

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