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.
•
written
by
Cy •
3 answers
Use the igraph R package. There's a great tutorial on using it for visualization.
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)
ggraph use ggplot2 and igraph to plot nice networks in R : https://github.com/thomasp85/ggraph
Why not use Cytoscape? http://www.cytoscape.org/
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