`vignettes/Cytoscape-and-iGraph.Rmd`

`Cytoscape-and-iGraph.Rmd`

This vignette will show you how to convert networks between igraph and Cytoscape.

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

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

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")`

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 yourselfâ€¦

```
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.**