Question: Cytoscape: Plot Custom Images Above Edges
gravatar for Timtico
7.4 years ago by
Timtico330 wrote:

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.

java cytoscape • 2.4k views
ADD COMMENTlink modified 7.4 years ago by paul.thurmond.shannon0 • written 7.4 years ago by Timtico330
gravatar for Josh Herr
7.4 years ago by
Josh Herr5.7k
University of Nebraska
Josh Herr5.7k wrote:

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?

ADD COMMENTlink written 7.4 years ago by Josh Herr5.7k
gravatar for paul.thurmond.shannon
7.4 years ago by
paul.thurmond.shannon0 wrote:

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.


  • Paul

RCytoscape makes this easy, if you know (or wish to learn) R. For lots of documentation, see
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

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

  • Paul
ADD COMMENTlink written 7.4 years ago by paul.thurmond.shannon0
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