Question: Solution For The Display Of Multi Dimensional Expression Data In Cytoscape?
2
gravatar for Timtico
8.7 years ago by
Timtico330
NL
Timtico330 wrote:

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?

cytoscape • 2.2k views
ADD COMMENTlink written 8.7 years ago by Timtico330
1
gravatar for David Quigley
8.7 years ago by
David Quigley11k
San Francisco
David Quigley11k wrote:

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.

ADD COMMENTlink written 8.7 years ago by David Quigley11k

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.

ADD REPLYlink written 8.7 years ago by Timtico330

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.

ADD REPLYlink written 8.7 years ago by David Quigley11k

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 :)

ADD REPLYlink written 8.7 years ago by Timtico330
1
gravatar for Chris Evelo
8.7 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

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

ADD COMMENTlink written 8.7 years ago by Chris Evelo10.0k

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.

ADD REPLYlink written 8.7 years ago by Timtico330

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

ADD REPLYlink written 8.7 years ago by Chris Evelo10.0k

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

ADD REPLYlink written 8.7 years ago by Timtico330
0
gravatar for Qdjm
8.7 years ago by
Qdjm1.9k
Toronto
Qdjm1.9k wrote:

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

ADD COMMENTlink written 8.7 years ago by Qdjm1.9k

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

ADD REPLYlink written 8.7 years ago by Timtico330
0
gravatar for Keiichiro Ono
8.5 years ago by
Keiichiro Ono130
San Diego, CA
Keiichiro Ono130 wrote:

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.

ADD COMMENTlink modified 8 months ago by RamRS27k • written 8.5 years ago by Keiichiro Ono130
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