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 start?
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.
- Alex
From: Yin Jun <yinjun...@gmail.com>
Reply-To: Cytoscape-Discuss <cytoscape-discuss@googlegroups.com>
Date: Sunday, October 14, 2012 7:15 PM
To: Cytoscape-Discuss <cytoscape-discuss@googlegroups.com>
Subject: [Cytoscape-discuss] How can I add shadow to a group of nodes?
Hi,
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
start?
Cheers,
Jun
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Thx for your information. I mainly use perl for programming purpose. My Java knowledge is very basic. I will start from Prefuse and see what I can do about it.
On Sunday, October 14, 2012 10:40:54 PM UTC-4, Alexander Pico wrote:
> Hi Jun,
> 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.
> - Alex
> From: Yin Jun <yinj...@gmail.com <javascript:>> > Reply-To: Cytoscape-Discuss <cytoscap...@googlegroups.com <javascript:>> > Date: Sunday, October 14, 2012 7:15 PM > To: Cytoscape-Discuss <cytoscap...@googlegroups.com <javascript:>> > Subject: [Cytoscape-discuss] How can I add shadow to a group of nodes?
> Hi,
> 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 start?
> Cheers, > Jun
> -- > You received this message because you are subscribed to the Google Groups > "cytoscape-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/cytoscape-discuss/-/3lqTEIlIJOYJ. > To post to this group, send email to cytoscap...@googlegroups.com<javascript:> > . > To unsubscribe from this group, send email to > cytoscape-disc...@googlegroups.com <javascript:>. > For more options, visit this group at > http://groups.google.com/group/cytoscape-discuss?hl=en.
