Solution For The Display Of Multi Dimensional Expression Data In Cytoscape?

Question

[Timtico]

I've build a network in cytoscape. I've annotated edges (gene names) with expression values. Now this works fine for single expressionvalues. But I'm looking for a way to show multiple expressionvalues next to an edge. I could do this in a basic way e.g: gene_ID (expression1, expression2, expression3).

However, I would prefer something that is abit more visual. For example, it would be nice to have a little heatmap consisting of four squares displayed next to each edge, representing the expressionlevel of that certain gene at different conditions.

Is there a solution for this in cytoscape? I've been browsing the plugins but could not find anything useful?

Answer 1

[David Quigley]

To my knowledge you can choose images for nodes but not for edges: documentation on the custom graphics manager. I typically represent genes as nodes rather than edges, but that might not work for you. You can key edge width, color, and style to continuous variables.

[Timtico]

Yeah, I'm aware you can chose images for nodes, but each node is a compound in my network. The edges are the different enzymes/gene_ID's that are responsible for the reactions.

[David Quigley]

Perhaps you can finesse it by putting a gene node between two reaction nodes, and assigning the desired figure to the gene node. Might complicate layout algorithms, but for a small figure it would probably work.

[Timtico]

that could work, but it would complicate the networks actually. So basically i'm waiting for someone to write a plugin that lets me annotate edges :)

Answer 2

[Chris Evelo]

You can actually show "chart generated" data in Cytoscape nodes, so you could for instance used X,Y graphs or radar charts.

[Timtico]

indeed that works well for the nodes, but not for the edges i'm afraid. I'm interested if someone could make a plugin where i can add graphics to edges.

[Chris Evelo]

Sorry should have read more carefully. So, if your edges are genes, what do you have in the nodes? What is it that the genes connect

[Timtico]

my nodes are different chemical compounds, the edges are genes encoding the enzymes that lead from one compound (source) to the target.

Answer 3

[Qdjm]

How about using multiple edges, distinguished by colour, between each pair of nodes? You could indicate expression level by thickness.

[Timtico]

Might be a good solution, but it might get a bit clunky. I will try it tonight :)

Answer 4

[Keiichiro Ono]

I recommend this plugin by UCSF: Node Chart Plugin

This uses basic Custom Graphics feature in Cytoscape, so you can easily save and restore visualizations.