Hi,
This question is about network analysis workflows and how to properly
integrate different tools for network analysis and network
visualization. I was not sure where to post this question, but since
igraph is most central to my workflow and I'm going to stick with it, I
decided to post here.
Currently I'm using igraph for R, gephi <http://gephi.org/> and recently
sometimes RedeR
<http://www.bioconductor.org/packages/2.14/bioc/html/RedeR.html>.
Normally, when doing exploratory network analysis I build my network in
R > igraph and run some basic statistics e.g. degrees or other
centrality measures and append these values as attributes to the
vertices. Afterwards I export the graph as graphml and load it into
gephi where I start to explore it. After that I get back to igraph and
start to test the generated hypothesis.
I use Gephi because of the following reasons. First of all because of
its layout algorithms, which manage to layout huge graphs, and most of
my graphs are rather large. Secondly because of the community of
developers behind it who constantly come up with new plugins and
features. Honestly I like it also, because it produces beautiful
outcomes. What I don't like about is its gui. I would prefer to
manipulate graphs from within igraph.
If my graph isn't very large I use RedeR, which I discovered recently.
In my opinion this is the perfect way to explore graphs. RedeR
establishes a stable connection between igraph and a java visualization
engine. This allows you to fully manipulate the graph from the R
console, but you can also select nodes with the mouse and get your
selection of nodes back into R, where you can run further analysis on them.
My little pipe dream is a RedeR-like extension for igraph with gephi
layout algorithms. So here are some first ideas to get to that.
+Gephi has a plugin <http://gephi.org/index.php?s=streaming> which
allows to stream graphs into Gephi. If I understand that right there is
a way to stream graphs to gephi in igraph for Python?
<http://igraph.sourceforge.net/doc/python/igraph.remote.gephi.GephiGraphStreamer-class.html>
+Gephi toolkit <https://gephi.org/toolkit/> is a Java library which be
can used to control gephi. This might be a way to automate things by
calling this library from within R?
+Since RedeR and Gephi are Java maybe there is a way to use the Gephi
layout algorithms from within RedeR?
It would be great if someone could point me in the right direction!
I appreciate any help that you can provide
stephan
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