Question: Looking For Network Visualization Tools
3
gravatar for elb
6.4 years ago by
elb160
Torino
elb160 wrote:

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

network tool plot • 5.6k views
ADD COMMENTlink modified 6.4 years ago by zx87547.1k • written 6.4 years ago by elb160
5
gravatar for Pawel Szczesny
6.4 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

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.

CLANS screenshot

ADD COMMENTlink written 6.4 years ago by Pawel Szczesny3.2k

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

ADD REPLYlink written 6.4 years ago by elb160
2
gravatar for Ben
6.4 years ago by
Ben2.0k
Edinburgh, UK
Ben2.0k wrote:

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).

ADD COMMENTlink written 6.4 years ago by Ben2.0k

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

ADD REPLYlink written 6.4 years ago by elb160
2
gravatar for fanofactor
6.4 years ago by
fanofactor30
fanofactor30 wrote:

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

library(igraph)
g <- graph.adjacency(as.matrix(yourData), mode="undirected", weighted=TRUE)
ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by fanofactor30

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..

ADD REPLYlink written 6.4 years ago by elb160
1
gravatar for zx8754
6.4 years ago by
zx87547.1k
London
zx87547.1k wrote:

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

ADD COMMENTlink written 6.4 years ago by zx87547.1k

Hi zx8754! What a fantastic tool!!!

ADD REPLYlink written 6.4 years ago by elb160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1109 users visited in the last hour