Installation

if(!"RCy3" %in% installed.packages()){
    install.packages("BiocManager")
    BiocManager::install("RCy3")
}
library(RCy3)
library(igraph)

Required Software

The whole point of RCy3 is to connect with Cytoscape. You will need to install and launch Cytoscape:

• Download the latest Cytoscape from http://www.cytoscape.org/download.php
• Complete installation wizard
• Launch Cytoscape

cytoscapePing()

From igraph to Cytoscape

The igraph package is a popular network tool among R users. With RCy3, you can easily translate igraph networks to Cytoscape networks!

Here is a basic igraph network construction from the graph_from_data_frame docs, http://igraph.org/r/doc/graph_from_data_frame.html:

actors <- data.frame(name=c("Alice", "Bob", "Cecil", "David",
                            "Esmeralda"),
                     age=c(48,33,45,34,21),
                     gender=c("F","M","F","M","F"))
relations <- data.frame(from=c("Bob", "Cecil", "Cecil", "David",
                               "David", "Esmeralda"),
                        to=c("Alice", "Bob", "Alice", "Alice", "Bob", "Alice"),
                        same.dept=c(FALSE,FALSE,TRUE,FALSE,FALSE,TRUE),
                        friendship=c(4,5,5,2,1,1), advice=c(4,5,5,4,2,3))
ig <- graph_from_data_frame(relations, directed=TRUE, vertices=actors)

# if function not found, then you need to install igraph. Try library(igraph)

You now have an igraph network, g. In order to translate the network together with all vertex (node) and edge attributes over to Cytoscape, simply use:

createNetworkFromIgraph(ig,"myIgraph")

From Cytoscape to igraph

Inversely, you can use createIgraphFromNetwork() in RCy3 to retrieve vertex (node) and edge data.frames to construct an igraph network.

ig2 <- createIgraphFromNetwork("myIgraph")

Compare the round-trip result for yourself…

ig
ig2

Note that a few additional attributes are present which are used by Cytoscape to support node/edge selection and network collections.

Also note: All networks in Cytoscape are implicitly modeled as directed. This means that if you start with an undirected network in igraph and then convert it round-trip (like described above), then you will end up with a directed network.