Looking For Network Visualization Tools

Question

[elb]

Hi to all. I would like to plot a network of interacting genes. I performed Mutual Information between genes starting from gene expression values, so my adjacency matrix is composed of mutual information values. Now I would like to have a visualization of the interactions. I tried to use Cytoscape or R igraph or RCytoscape but all this methods transform the adjacency matrix in a boolean matrix. Is there a way or a tool that does not transform the adj matrix in a boolean one? This because according to the mutual information value I would like to have different lengths in edges. For example if A and B interact with a mutual information value of 0.20, the edge connecting them will be longer than the edge connecting A and C that show a mutual information of 0.1.

Any suggestion about this?

Thank you in advance

Answer 1

[Pawel Szczesny]

You might be interested in CLANS software. It performs clustering (2D or 3D) based on distance matrix (exactly what you have) and has a support for microarray experiments.

[elb]

Hi Pawel!! It is a fantastic tool! thank you sooo much!!

Answer 2

[Ben]

Sounds like you have a distance matrix rather than an adjacency matrix, I've not used cytoscape but it looks like it's easy to make a graph with weighted edges by modifying your input format slightly (link).

[elb]

Hi Ben!! yes, I suppose it is more like a distance matrix than an .adj matrix!

Answer 3

[fanofactor]

I have used similar data without a problem with igraph. Try:

library(igraph)
g <- graph.adjacency(as.matrix(yourData), mode="undirected", weighted=TRUE)

[elb]

Hi fanofactor!!! Thank you for your help! Unfortunately while I solved the problem of MI values setting weighted = T, I encountered another problem because that function (graph.adjacency) needs a squared matrix, and my matrix is not a squared one..

Answer 4

[zx8754]

Try Gephi - an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. https://gephi.org/

[elb]

Hi zx8754! What a fantastic tool!!!