---
title: "Cytoscape and graphNEL"
author: "by Alexander Pico"
package: RCy3
date: "`r Sys.Date()`"
output: 
  BiocStyle::html_document:
    toc_float: true
vignette: >
  %\VignetteIndexEntry{3. Cytoscape and graphNEL}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
  eval=FALSE
)
```

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

# Installation
```{r}
if(!"RCy3" %in% installed.packages()){
    source("https://bioconductor.org/biocLite.R")
    biocLite("RCy3")
}
library(RCy3)
```

# 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 

```{r}
cytoscapePing()
```

# 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
```{r}
g <- makeSimpleGraph()
```

Now pass it along to Cytoscape:

```{r}
createNetworkFromGraph(g,"myGraph")
```
# From Cytoscape to GraphNEL 
Inversely, you can use createGraphFromNetwork() in RCy3 to retreive vertex (node) and edge data.frames to construct a GraphNEL object. 

```{r}
g2 <- createGraphFromNetwork("myGraph")
```

Compare the round-trip result for yourself...
```{r}
g
g2
```
