how to visualize the path between two nodes

[fadlyemen]

Hi
If I have two nodes x1 and x10 and they connect via another nodes x2,
x3,...
Is there any plugin which when I select two nodes it highlight the
path between these two nodes.
It is like google earch two country you can see the ways betwen them.
Second when I select node by ctrl F and if my network is large so I
could not see my node especially when it has low edge count, so is
there plugin when i select my node it pop up.
Regards

[allan_k...@agilent.com]

There is a ShortestPaths plugin that is accessible from the plugins page on the Cytoscape web site (http://chianti.ucsd.edu/cyto_web/plugins/index.php). Look under Analysis section. Evidently it has not yet been verified to run under the most recent version of Cytoscape (2.6.2), but I just tried it out and it worked for me. You need to download the jar file from that page and copy it into the plugins directory under your Cytoscape installation. Use Plugins -> Shortest path... -> Shortest Path (undirected) menu item after selecting two nodes.

As for your second question, Cytoscape's QuickFind functionality does exactly what I think you want. Just start typing in the text box to the right of the Search: label. For example, enter "yd". The search box will automatically display a list of all matching nodes. Select a matching node. Cytoscape will automatically zoom in on the selected node. For more information, you can look at the chapter on Finding and Filtering Nodes and Edges in the Help documentation.

Let me know if this information is helpful.

AllanK





Allan Kuchinsky
Principal Project Scientist
Molecular Tools  
Agilent Laboratories

Agilent Technologies, Inc.
Santa Clara, CA, USA
408.553.2423
allan_k...@agilent.com

[fadlyemen]

Yes it works perfectly, Thanks a lot.
I wish after I select the two nodes, the pathway between them and the
nodes crossing them is being bold so if my network is large I could
see the pathway.
Also Is there solving for old plugin, becuse some usfual plgin works
with cytoscape 2.4, so you have to install 2.6, 2.5 and 2.4.
Regards

On Jun 14, 7:48 pm, <allan_kuchin...@agilent.com> wrote:
> There is a ShortestPaths plugin that is accessible from the plugins page on the Cytoscape web site (http://chianti.ucsd.edu/cyto_web/plugins/index.php).  Look under Analysis section.  Evidently it has not yet been verified to run under the most recent version of Cytoscape (2.6.2), but I just tried it out and it worked for me.  You need to download the jar file from that page and copy it into the plugins directory under your Cytoscape installation.  Use Plugins -> Shortest path... -> Shortest Path (undirected) menu item after selecting two nodes.
>
> As for your second question, Cytoscape's QuickFind functionality does exactly what I think you want.  Just start typing in the text box to the right of the Search: label. For example, enter "yd". The search box will automatically display a list of all matching nodes.  Select a matching node. Cytoscape will automatically zoom in on the selected node.  For more information, you can look at the chapter on Finding and Filtering Nodes and Edges in the Help documentation.
>
> Let me know if this information is helpful.
>
> AllanK
>
> Allan Kuchinsky
> Principal Project Scientist
> Molecular Tools  
> Agilent Laboratories
>
> Agilent Technologies, Inc.
> Santa Clara, CA, USA
> 408.553.2423

> allan_kuchin...@agilent.com