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.

Weiwei

On Sat, May 28, 2011 at 11:51 AM, Weiwei Shi <helprhelp@gmail.com> wrote:

> Thank you, Steve.
>
> Initially I tried to choose b/w cytoscape and pajek, among other bunch of
> software. I did not realize the existence of RCytoscape; otherwise, I would
> probably use that one.
>
> Weiwei
>
>
> On Sat, May 28, 2011 at 9:25 AM, Steve Lianoglou <
> mailinglist.honeypot@gmail.com> wrote:
>
>> Hi,
>>
>> On Fri, May 27, 2011 at 5:32 PM, Weiwei Shi <helprhelp@gmail.com> wrote:
>> > Hi there,
>> >
>> > I need a network builder and it can change the node size and color; I am
>> not
>> > sure if network package in R can do this or not. The other functions I
>> > wanted have been found in that package.
>> >
>> > BTW, if there is another package in R relating to this, please suggest
>> too.
>>
>> I'm not actually sure what you're looking for, but from trying to
>> piece together the other emails in this thread maybe you are looking
>> for a way to control graph/network layout in some GUI form?
>>
>> There is a bioconductor package called RCytoscape that can "drive"
>> cytoscape from R, allowing you to draw a network you have loaded up in
>> your R session and tweak different properties of nodes, edges, etc:
>>
>> http://www.bioconductor.org/packages/release/bioc/html/RCytoscape.html
>>
>> Maybe it can help you? I'm not sure if this is what you're asking for,
>> though, so I could be way off the mark.
>>
>>
>> HTH,
>> -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
>>
>
>
>
> --
> Weiwei Shi, Ph.D
> Research Scientist
>
>
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
>



-- 
Weiwei Shi, Ph.D
Research Scientist


"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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