In cytoscape/r2cytoscape: Functions for Cytoscape Automation

This vignette will show you how to connect to Cytoscape from R using CyREST. It will cover the installation of required packages and demonstrate some basic functionality of CyREST, commands and r2cytoscape.

It is recommended that your run this vignette prior to Cytoscape Automation workshops to mitigate troubleshooting time.

Installation

source("https://bioconductor.org/biocLite.R")
biocLite("r2cytoscape")

Required Software

The whole point of r2cytoscape is to connect with Cytoscape. You will need to install and launch Cytoscape:

• Download Cytoscape
• Complete installation wizard
• Launch Cytoscape

First Contact

This function is a convenient way to verify a connection to Cytoscape. It is also helpful for logging the versions of CyREST and Cytoscape in your scripts.

checkCytoscapeVersion()

My First Network

Let's create a Cytoscape network from some basic R objects

mynodes <- data.frame(id=c("node 0","node 1","node 2","node 3"), 
                      group=c("A","A","B","B"), # optional
                      stringsAsFactors=FALSE)
myedges <- data.frame(source=c("node 0","node 0","node 0","node 2"), 
                      target=c("node 1","node 2","node 3","node 3"),
                      interaction=c("inhibits","interacts","activates","interacts"),  # optional
                      weight=c(5,3,5,9), # optional
                      stringsAsFactors=FALSE)
network.name = "myNetwork"
collection.name = "myCollection"

network.suid <- createNetwork(mynodes,myedges,network.name,collection.name)

Switch Styles

Check out the marquee style!

applyStyle('Marquee')

My Own Style

Create your own style with node attribute fill mappings and some defaults

style.name = "myStyle"
defaults <- list(NODE_SHAPE="diamond",
                 NODE_SIZE=30,
                 EDGE_TRANSPARENCY=120,
                 NODE_LABEL_POSITION="W,E,c,0.00,0.00")
nodeLabels <- mapVisualProperty('node label','id','p')
nodeFills <- mapVisualProperty('node fill color','group','d',c("A","B"), c("#FF9900","#66AAAA"))
arrowShapes <- mapVisualProperty('Edge Target Arrow Shape','interaction','d',c("activates","inhibits","interacts"),c("Arrow","T","None"))
edgeWidth <- mapVisualProperty('edge width','weight','p')

createStyle(style.name, defaults, list(nodeLabels,nodeFills,arrowShapes,edgeWidth))
applyStyle(style.name)

Browse Available Commands and Arguments

r2cytoscape helper functions

help(package=r2cytoscape)

Open swagger docs for live instances of CyREST API and CyREST-supported commands:

openCySwagger()  # CyREST API
openCySwagger("commands")  # CyREST Commands API

List available commands and arguments in R. Use "help" to list top level:

commandHelp("help")  

List network commands. Note that "help" is optional:

commandHelp("help network")  

List arguments for the network select command:

commandHelp("help network select") 

Those are the basics. You are now ready to work with some real data! See other basic and advanced R tutorials.

cytoscape/r2cytoscape documentation built on May 4, 2019, 6:36 p.m.