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