Dear All, I have two networks. Both the networks have common nodes as well as unique nodes. Is there any way I can combine both and analyze??
4 answers
Using R igraph union:
library(igraph)
net1 <- graph_from_literal(A-B:C:D, A-C, B-C)
net2 <- graph_from_literal(A-X:Y:Z, Z-Y)
par(mfrow = c(1, 3))
set.seed(1)
plot(net1, vertex.size = 50, main = "net1")
plot(net2, vertex.size = 50, main = "net2")
plot(union(net1, net2), , vertex.size = 50, main = "union of net1 and net2")
Sure. Read both networks into Cytoscape, and then use the Network Merge tool to do a Union. The resulting network should be what you want.
-- scooter
A couple of examples from the literature:
- Combining sRNA-gene and TF-gene networks: https://academic.oup.com/nar/article/43/3/1357/2411571
- TF-gene and PPi networks: https://www.pnas.org/content/101/16/5934.short
If they are in the form of edge-lists, you can append the two edge lists one after another and make a common edgelist. Then load it in Cytoscape and there is an option to remove duplicate edges. Don"t forget to add node and/or edge attributes to know which gene/edge is unique or common. Based on this, you can color your nodes/edges differently. HTH.
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