specify edge attributes in SIF file?

[RJo]

Hello,

Is there a way to specify edge attributes (such as colour of an edge)
in a SIF file? For example, I have the a binary matrix of following
format (representing a gene network)(tab delimited file)

GeneA GeneB S Category1 Category2 Category3
sifA transA 1 1 0 1
tom2 ypd3A 2 1 1 0
tom3 ypd3A 3 0 1 0
rah3 gatA 3 0 1 0
...

...and I've created a perl script that converts the above matrix to a
sif format file as follows:

sifA Category1 transA
sifA Category3 transA
tom2 Category1 ypd3A
tom2 Category2 ypd3A
...

However, I would like to add additional attributes to these edges, in
particular, colour all edges with a value of 3 in the "S column" with
the colour red, all the ones with S value of 2 with colour green...etc.

Any ideas?

R.Jo

[Rowan Christmas]

I have been working on a Plugin that allows exactly this sort of
loading. The format for it is:

NODENAME <node attributes>
(nodes and attributes go here)
NODENAME EDGETYPE NODENAME <edge attributes>
(edges and attributes go here, with the Nodes specifying the edges
using the same identifiers in both sections.)

so your example spread sheet would load just fine after changing the
first few column headings. You would only need this file, and not an
additional SIF file.

it only works with the latest CVS versions of Cytoscape. You can
compile it from CVS form csplugins/isb/xmas/loader, or I can send you
a jar.

To load from the command line use "-ss <name of file>" where the file
is saved as tab-delimited text. Or use "File->Load->Load Network". The
plugin also saves networks back using the same format.

Let me know if you have questions, I would love to have someone using
CVS be able to test this out for me a little more.

--rowan

[RJo]

Interesting...would you mind sending me the plugin/link to the plugin
and a detailed description on how to modify my matrix file to be so
that it can be read into cytoscape. Also, would you happen to know if
there is a way to launch cytoscape (and the plugin) from the browser so
that there is no download/installation needed for users....

R.

[Rowan Christmas]

you can make a webstart version. Search this list for what the latest
on that is....I am honestly not exactly sure.

http://cytoscape.org/cgi-bin/moin.cgi/CVS_Access

is our wiki page on how to get the latest anonymous CVS version. My
plugin is not really ready for super-primetime just yet. But feel free
to grab the source, and let me know any compile errors you may have.

--rowan

On 11/28/05, RJo <rsa...@gmail.com> wrote:
>

[RJo]

Im not really sure how to compile cvs versions of cytoscape...do you
happen to have/know where I can get the full compiled version of
cytoscape? If so, please let me know.

THanks again,
R

[Rowan Christmas]

If you are not comfortable with compiling, then you should use the
released version. Available from cytoscape.org.

[RJo]

Sure! Does that one include ure plugin?

[RJo]

Now, that i've got cytoscape installed, how do i load it in using your
plugin ? (the above instructions u've provided seem to be for loading
networks in general)

[RJo]

And would it be possible for you to send me a .jar file fo the plugin
please?

Thanks,
R