[R] network package in R

[Steve Lianoglou]

Hi again,

On Sat, May 28, 2011 at 1:03 PM, Weiwei Shi <helprhelp at gmail.com> wrote:
> Actually I have another question relating to this,
>
> I have about 300 nodes (I can reduced them somehow if the network is too
> messy) and the similarity matrix between any two nodes. The size and color
> of nodes have some meanings and I tried to use the layout to show their
> "distance".
>
> Here is the question:
>
> for example, there are nodes A, B and C. There is a threshold to define if
> there is a link or not between nodes. Let's assume there are links between A
> and B; and A and C. There is no link between B and C. However, when there
> are more nodes added, the physical distance on the plot between B and C is
> shorter than some other linked pair, for example, C and D. I was suggested
> it was due to the layout algorithm: because A-B and A-C links, so B and C
> were pulled nearer. I am not sure if there is a better solution or not. I
> mean, physically B and C look nearer than C-D, although the latter has a
> link while B and C do not.
>
> I hope I explained my question clear this time.

I actually don't have a direct answer to your question -- and this
isn't even related to R, but the following has hit my radar recently
and thought it might be helpful:

http://www.hiveplot.org/

It's a different way to visualize (large) networks that uses some of
the networks structure in order to make it more visually interpretable
(once you understand how to interpret them!) than normal graph
visualizations allow -- to put it another way, it avoids the hairball
effect.

It sounds like you're struggling to plot things in one way, but the
layout algorithms all want to make you see it another ... so maybe
this option will be helpful.

Also, you might get better "graph layout" suggestions on mailing lists
that are focused on working with graphs. I'm pretty sure cytoscape has
a mailing list you can ping, and there is also igraph (which has an R
interface) which has its own mailing list ... maybe the pros there can
help provide more insight.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact