Construction of network diagrams by using R

Question

[Cy]

Greeting.

I want to create a network by using R but I only have a table that contain OTU ID and the abundance value of two samples ONLY.

Isn't possible? If can, which package can be used or any other software? Greatly appreciated to any suggestions and helps.

Thank you.

Answer 1

[Jean-Karim Heriche]

Use the igraph R package. There's a great tutorial on using it for visualization.

[Cy]

Thank you for your suggestion. But I do not have the edge list and adjacent matrix. Hence, how to get the adjacent matrix in R.

[Jean-Karim Heriche]

You have to decide on how you want to represent your data as a graph. You can think of the adjacency matrix as being a similarity matrix. You could measure how similar OTUs are across the samples using a relevant similarity measure (for similarity measures in R, see the proxy package)

Answer 2

[Nicolas Rosewick]

ggraph use ggplot2 and igraph to plot nice networks in R : https://github.com/thomasp85/ggraph

Answer 3

[blackjack666]

Why not use Cytoscape? http://www.cytoscape.org/