Node color

[roelq]

Dear,

 

I am new to EGAN and have a couple of questions:

 

- is it possible to have node colors (instead of node border colors) depending on statistics, and then node border color depending on involvement in a certain pathway

- is it possible to have edge thickness depending on number of co-occurences in the literature

- how should I create new edges between two nodes

- how can I change the lay-out of selected nodes from the network (i.e. a network of 100 nodes of which I want 20 to have a circular lay-out around an association node) 

 

Hope you can help.

 

Cheers,

Roel

[ucsf egan]

Hi Roel,

Here are answers to your questions:

- It is not a great idea to use multiple colors in a node.  This is why we opted to show the statistic on the node and display pathway/annotation as hypernodes.  See Figure 1 http://akt.ucsf.edu/EGAN/docs/PSI78650E.pdf  Other softwares use a combination of shapes and colors - this is currently not available in EGAN.

- Changing edge thickness is a good idea, but unfortunately not possible in EGAN.

- You can specify edges using the .SIF format.  See http://akt.ucsf.edu/EGAN/docs/EGAN_tutorial_Loading_network_data.pptx

- There is a layout menu to the left of the network view.  Hopefully one of those options will suffice for your needs.

Thanks!  By the way, if you want full customizability for graph attributes, you should consider using Cytoscape directly.  EGAN is built for streamlined interpretation of experiment results using a straightforward and simple paradigm.

Best,

Jesse