---
title: "Shortest Path with RBGL"
author: "by Alexander Pico"
date: "`r Sys.Date()`"
output:
  html_notebook:
    toc_float: yes
    code_folding: none
  html_document:
    df_print: paged
package: RCy3
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
  eval=FALSE
)
```

*The R markdown is available from the pulldown menu for* Code *at the upper-right, choose "Download Rmd", or [download the Rmd from GitHub](https://raw.githubusercontent.com/cytoscape/cytoscape-automation/master/for-scripters/R/notebooks/Shortest-path.Rmd).*

This vignette will show you how to perform a shortest path calculation using RBGL on a network in Cytoscape. RBGL is a Biocondutor package that offers an array of analytical functions for graphs.

# Installation
```{r eval=FALSE}
if(!"RCy3" %in% installed.packages()){
    install.packages("BiocManager")
    BiocManager::install("RCy3")
}
if(!"RBGL" %in% installed.packages()){
    install.packages("BiocManager")
    BiocManager::install("RBGL")
}
library(RCy3)
library(RBGL)
```

# 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()
```

# Shortest Path with RBGL
<center>
![](https://cytoscape.github.io/cytoscape-automation/for-scripters/R/notebooks/data/img/shortest.png)
</center>

Convert a sample Cytoscape network to a graph object (after removing a multiedge).
```{r}
openSession()
selectEdges("YPL248C (pp) YML051W","name")
deleteSelectedEdges()
g <- createGraphFromNetwork()
```
	
Identify start and finish nodes (styling is optional).
```{r}
start <- "YNL216W"  #RAP1
finish <- "YER040W"  #GLN3
setNodeBorderWidthBypass(c(start,finish), 20)
setNodeBorderColorBypass(start,"#00CC33")
setNodeBorderColorBypass(finish,"#CC00CC")
```

Perform shortest path calculation.
```{r}
shortest <- sp.between(g, start, finish)
shortest$`YNL216W:YER040W`$length 
shortest.path <- shortest$`YNL216W:YER040W`$path_detail
```

Visualize results in Cytoscape.
```{r}
selectNodes(shortest.path, "name")
setNodeBorderWidthBypass(shortest.path, 20)
createSubnetwork()
```