Re: [igraph] tkplot() - error message

[Tamas Nepusz]

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