The Cerebral plugin used an external toolkit called Prefuse to create many
of the unique visual effects. I believe this includes the background
"shadow" you refer to that is around clustered groups of nodes. It is not
part of Cytoscape or the VizMapper.
That being said, since Cerebral was released a lot of work has been done on
representing groups of nodes in Cytoscape. There is now a Groups concept in
the core model of Cytoscape and a few features like expand/collapse via the
Metanode2 plugin. I know adding support for a background color surrounding
groups is on the list of desired features, but not sure of the timeline. If
you have programming experience and time to contribute to this open source
work, I'd be happy to coordinate and help mentor the work.
From: Yin Jun <yinjun...@gmail.com>
Reply-To: Cytoscape-Discuss <firstname.lastname@example.org>
Date: Sunday, October 14, 2012 7:15 PM
To: Cytoscape-Discuss <email@example.com>
Subject: [Cytoscape-discuss] How can I add shadow to a group of nodes?
I used a cool cytoscape plugin called "cerebral". It provided a very useful
function of grouping different genes (nodes) by functions, and add shadow to
this group of genes. I cann't find this "shadow" option in the Vizmapper in
the cytoscape. Do you know how I can add shadow by myself to a group of
selected nodes? If I have to write some scripts by myself, where should I
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