Re: [igraph] tkplot() - error message

[Tamas Nepusz]

Dear Diana,

First I'd try to normalize the layout matrix so that both the X and Y  
coordinates are within a reasonable range:

layout <- layout.norm(pub.mat, xmin=0, xmax=1, ymin=0, ymax=1)
tkplot(graph, layout=layout)

This probably won't look too good as the PubMed IDs and the years  
might be correlated (an article that's published later will have a  
higher PubMed ID, so the X and Y coordinates will be positively  
correlated). But I guess it's a good starting point.

--
Tamas

On 2009.09.23., at 16:05, Diana Neufeld wrote:

> Dear Tamas, dear all,
>
>
> thanks for your answer.
> My matrix contains PubMedID’s in the first column and the  
> ArticleDate in the second.
> So what I want is to get a graphic with a y-axis and vertices  
> depends on time (ArticleDate).
> The additional information I have: publications and their references  
> (data frame with two columns).
> How can I use this time-information to get a graph, whose vertices  
> are not randomly placed on a
> window opened by tkplot().
> And if I rename my PubMedID’s in short notations, so it could work?
>
> Thanks, Di.
>
>
>
>
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: "Tamas Nepusz" <address@hidden>
> > Gesendet: 23.09.09 16:14:46
> > An: Help for igraph users <address@hidden>
> > Betreff: Re: [igraph] tkplot() - error message
>
>
> > Dear Diana,
> >
> > > > tkplot(graph , layout=pub.mat)
> > > [..]
> > > pub.mat  is a matrix with two columns like this:
> > >
> > >   pubMedID ArticleDate
> > > 12    53631           11
> > > 15   475066          14
> > The layout() argument of tkplot needs a graph layout; it is a matrix
> > with N rows and two columns, the first column containing the X
> > coordinate of the node on the plot, the second column containing  
> > the Y
> > coordinate. Your matrix does not look like a valid layout. igraph
> > tries to interpret it as a layout, so the PubMed IDs will be  
> > treated as
> > X coordinates, but they are too large.
> > What you will have to do is:
> >
> > Either call tkplot() without the layout= option and set a layout from
> > the menu of the window opened by tkplot() -- you can also rearrange  
> > the
> > nodes by the mouse if you don't like the layout generated by igraph.
> > Alternatively, you can pre-calculate a layout using igraph's various
> > layout methods and pass the matrix obtained from the layout  
> > function. An
> > example:
> >
> > layout <- layout.fruchterman.reingold(graph)
> > tkplot(graph, layout=layout)
> >
> > Best,
> > --
> > Tamas
> >
> >
> > _______________________________________________
> > igraph-help mailing list
> > address@hidden
> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>
>
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