R_cytoscape_tutorial

Tutorial on using R to run cytoscape visualizations

UPDATE: just found out about RCy3 which could greatly simplify the code used run Cytoscape from R: https://www.bioconductor.org/packages/release/bioc/html/RCy3.html

• Will update the tutorial soon.

There are lots of great ways to make simple networks in R. A non-exhaustive list includes:

• Diagrammer https://github.com/rich-iannone/DiagrammeR
• igraph http://igraph.org/r/
• ggraph https://github.com/thomasp85/ggraph

This tutorial is aimed at:

• Cytoscape users interested in running/automating the creation and manipulation of Cytoscape networks using R.
• R users interested in examining more complex networks in an exploratory way
• R users interested in visualizing networks with metadata.

The tutorial will:

• Get R and Cytoscape "talking"
• Build a small network in R
• Send the network to Cytoscape
• Give a brief tour of the network in Cytoscape
• Style network visualization using network properties and metadata