Cytoscape: Plot Custom Images Above Edges

Question

[Timtico]

In my cytoscape network I would like to plot small custom images (barcharts) above each edge. I cannot find a app in the appstore that suits my needs.

The workaround would be to have custom node pictures, I know I can select the graphics manually. But is there also a way to automate this. So it uses a specific graph for each node? I can then have a directory filled with barcharts images and automatically plot these as custom images on the nodes, without the need to do this manually for hundreds or thousands of network nodes :)

I hope my question is not too vague, thank you.

Answer 1

[Josh Herr]

Maybe I'm not fully understanding your question and no one has chimed in yet, but I am unaware of a package to automate just what you are interested in doing in Cytoscape.

I've done something similar very easily with my graphs as a vector output from R or matplotlib and place the images with your vector output from Cytoscape in a illustration interface (such as Adobe Illustrator), this was easy for me because I was only showing graphs for 20 nodes.

With the number of nodes you are considering, this sounds like you have a reasons to write a plugin now? Another thing to consider: is this the best way to visualize hundreds or thousands of graphs?

Answer 2

[paul.thurmond.shannon]

I did not scroll down enough to see this answer box. Not knowing how visible my edits (above) will be, I will try adding them here as well.

Cheers!

• Paul

RCytoscape makes this easy, if you know (or wish to learn) R. For lots of documentation, see http://rcytoscape.systemsbiology.net
Click on 'Examples' in the list found in the top left panel, then "'Informational' nodes: plots" in the list which appears in the lower left panel. Or go straight to http://db.systemsbiology.net:8080/cytoscape/RCytoscape/versions/current/cookbook/infoNodes-plots/index.html

RCytoscape is a Bioconductor package, now at version 1.8.2. I would be glad to answer questions if any arise.

• Paul