[R] igraph and plotting connected components
elw at stderr.org
elw at stderr.org
Tue Oct 9 03:11:16 CEST 2007
>> Hello there,
>> I am using the igraph package to build graphs from my data. If I plot
>> a graph though, it's not easy for me to see what's going on. Does
>> anybody know how to rearrange a graph to get a plot without too many
>> crossing lines? Maybe other packages?
Edge-crossing minimization is a research topic all in itself, for folks
who deal with graph-style data on a regular basis. ;-) It is *hard* to
construct sane graphs automatically, which is why software in this area so
frequently produces what appear to be sub-par results. [And it is
difficult for human beings to evaluate the 'quality' of such graphs,
comparatively - we just aren't good at this task.]
> Rgraphviz in Bioconductor does a great job of this. It's a wrapper for
> the Graphviz library, so the R docs are a little sparse, but there's a
> tremendous amount of flexibility there.
Seconded - graphviz in general is quite good; getting your data into
dot-file format is often a productive step in the viz process.
Dot-file format is also *ridiculously simple* to generate , which I think
of as a factor well in its favor. :-)
the dynamicGraph package (which I think lives in bioconductor as well) is
reasonably useful for smallish graphs.
I hear that there's a tk-based interactive graph layouter available with
graphviz's source - you might look there, too.
There's also Pajek, which is pretty and interactive but not R,
for-Windows, and not even very compatible with the data formats usually
used by folks with R. ;)
There's also the pixelglow build of graphviz on OSX, which is beautiful
and fun to mess with.
There are a couple other graph packages as well... most not interactive,
which sounds like what you're likely wanting.
[With some of the iterative graph rendering algorithms - particularly the
ones that deal with energy minimization algorithms and the like -
nondeterministic mostly - you can sometimes re-run the layout function and
get wildly different results, particularly for complex graphs. You might
school of library and information science
indiana university, bloomington
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