# Cytoscape and graphNEL

by Alexander Pico

#### 2024-11-25

#### Package

RCy3 2.27.0

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

# 1 Installation

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

# 2 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()

# 3 From graphNEL to Cytoscape

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

Create a simple GraphNEL object

    g <- makeSimpleGraph()

Now pass it along to Cytoscape:

    createNetworkFromGraph(g,"myGraph")

# 4 From Cytoscape to GraphNEL

Inversely, you can use createGraphFromNetwork() in RCy3 to retreive vertex (node) and edge data.frames to construct a GraphNEL object.

    g2 <- createGraphFromNetwork("myGraph")

Compare the round-trip result for yourself…

    g
    g2