How to visualize a network like in the provided example?

Question

[amjad]

Does anybody know how to plot a network similar to the one in the below TCGA paper?

http://www.nature.com/nature/journal/v517/n7536/fig_tab/nature14129_F5.html

More specifically, is there a tool to produce such visualization or was it created manually?

[Ashutosh Pandey]

I don't think there is a tool that needs to be specifically used for such figures. Adobe Illustrator would be a decent tool to generate such figures.

Answer 1

[Alex Reynolds]

Maybe you could make it with OmniGraffle. It has some nice network drawing tools. One thing that OmniGraffle offers that I don't think Illustrator offers is automatic management of connections between elements. For instance, you drag a node in the network and any connected edges are also redrawn. You can align nodes horizontally and vertically, to make a clean layout.

You might also investigate the SBGN format. One example in the relevant Nature paper shows stimulation and inhibition, for instance. It looks like an XML-based document format that might lend well to automation, if you are making lots of these figures.

[amjad]

Thank you, this was very useful. It seems to me that there is no way to escape the manual work.

Answer 2

[5utr]

Another option is Cytoscape

You can input nodes relationships in a simple table format ( and assign different arrow shapes to different relationships) as well as node characteristics (like in the example the % of activation) and use a color scale to automatically color the nodes.

[amjad]

Thanks. I am aware of cytoscape and the ability to color scale nodes. I wonder if there is a plugin to make the nodes as glyphs having two inner squares with different color scales.