Re: [igraph] vertex overlap layout

[Gábor Csárdi]

In the first case vertex frames are not hidden, but the vertices are
too small, you cannot see them, increase 'vertex.size' (units are
quite arbitrary). E.g.

plot(net,layout=clayout,edge.arrow.size=0.1,rescale=FALSE,xlim=c(1,500),ylim=c(1,400),
vertex.size=1000)

In the other case the edges between neighbors are below the vertices.
Decrease vertex size, e.g.

plot(net,layout=clayout,edge.arrow.size=0.1, vertex.size=5)

G.

On Wed, Mar 4, 2009 at 2:02 PM, Bruno Contreras Moreira
<address@hidden> wrote:
> 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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> _______________________________________________
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>
>



-- 
Gabor Csardi <address@hidden>     UNIL DGM