= Network Analysis in R with igraph =

A network can be described by a list of nodes, or vertices that interact with each other, thus a tab-delimited list:
{{{
Bj1	dah
Bj1	rst
Borr	CG6459
Borr	Rab11
BthD	CG6843
BthD	Mcm3
}}}

Read a table into R and generate a network graph:
{{{
data <- read.table(file="my_interactions.txt",sep="\t")

# create a graph data object
g <- graph.data.frame(data, directed=F)

# draw it
plot(g)
}}}

It can look a bit amorphous and un interpretable. Draw it with a "force-directed algorithm:
{{{
plot(g,layout=layout.fruchterman.reingold)
}}}

If your network contains un-connected pieces, you can find them using the deconstruct function.
{{{
dg <- decompose.graph(g)
}}}
This returns a list, whereby each element is itself a graph data object.