Awesome
RNeo4j 
RNeo4j is Neo4j's R driver. It allows you to read and write data from / to Neo4j directly from your R environment.
Contents
<img align="right" src="figure/RNeo4j-logo.png" />- Install
- Connect
- Nodes
- Relationships
- Cypher
- Shortest Paths
- Weighted Shortest Paths
- Graph Algorithms
- Visualizations
- Import
- Connection Issues
- Contribute
<a name="#install"></a>Install
Neo4j
First and foremost, download Neo4j!
Windows
If you're on Windows, download the .exe and follow the instructions. You'll get a GUI where you simply press "Start" to start Neo4j.
OS X
If you're on OS X, you can download either the .dmg or the .tar.gz. The .dmg will give you a GUI where you simply press "Start" to start Neo4j. Otherwise, download the .tar.gz, unzip, navigate to the directory and execute ./bin/neo4j start.
Linux
If you're on Linux, you have to use the .tar.gz. Download the .tar.gz, unzip, navigate to the directory and execute ./bin/neo4j start.
You may also find neo4j in your distribution's package manager.
Bolt dependencies
These depencies are are only required if you want to use the Bolt interface.
They must be present at build time, and libneo4j-client must also be present at runtime.
Windows
- Rust: https://rustup.rs
- Clang: binary releases are available at http://releases.llvm.org/download.html
- libneo4j-client:
- Make sure you have RTools installed (necessary for building R packages on Windows)
- Open your MinGW shell (check in start menu,
C:\RTools\MinGW\bin, andC:\MinGW\bin) - See "Installing libneo4j-from source" section
OS X (with Homebrew installed)
- Rust:
brew install rust(or https://rustup.rs but see "Rust Path" section) - Clang:
brew install llvm - libneo4j-client:
brew install cleishm/neo4j/libneo4j-client
Linux
- Rust:
- Debian based (e.g. Mint, Ubuntu):
sudo apt-get install cargo - Arch Linux:
sudo pacman -S rust - Building from source: https://rustup.rs but see "Rust Path" section
- Debian based (e.g. Mint, Ubuntu):
- Clang: get it from your package manager
- Debian based (e.g. Mint, Ubuntu):
sudo apt-get install clang libclang-dev - Arch Linux:
sudo pacman -S clang - Other: your package manager almost certainly has
clang. It may be calledllvm.
- Debian based (e.g. Mint, Ubuntu):
- libneo4j-client:
- Debian based:
sudo apt-get install libneo4j-client-dev - Other: See "Installing libneo4j-client from source"
- Debian based:
Rust Path
By default, on *nix systems (such as Linux and OS X), rustup only sets the PATH in your shell. That means that if you try to build RNeo4j in a GUI application like RStudio, it may fail. To work around this issue, simply build RNeo4j in a terminal.
Installing libneo4j-client from source
Newer versions of GCC require removing the -Werror from GCC_CFLAGS in configure.ac.
Run these commands in your shell:
git clone https://github.com/cleishm/libneo4j-client
cd libneo4j-client
./autogen.sh
./configure --disable-tools
sudo make install
See https://github.com/cleishm/libneo4j-client for more details
RNeo4j
From CRAN
install.packages("RNeo4j")
From GitHub
devtools::install_github("nicolewhite/RNeo4j")
From Source
Go to the latest release and download the source code. You can then install with install.packages.
install.packages("/path/to/file.tar.gz", repos=NULL, type="source")
Load the Package
library(RNeo4j)
<a name="#connect"></a>Connect
graph = startGraph("http://localhost:7474/db/data/")
If you have authentication enabled, pass your username and password.
graph = startGraph("http://localhost:7474/db/data/", username="neo4j", password="password")
<a name="#nodes"></a>Nodes
nicole = createNode(graph, "Person", name="Nicole", age=24)
greta = createNode(graph, "Person", name="Greta", age=24)
kenny = createNode(graph, "Person", name="Kenny", age=27)
shannon = createNode(graph, "Person", name="Shannon", age=23)
<a name="#relationships"></a>Relationships
r1 = createRel(greta, "LIKES", nicole, weight=7)
r2 = createRel(nicole, "LIKES", kenny, weight=1)
r3 = createRel(kenny, "LIKES", shannon, weight=3)
r4 = createRel(nicole, "LIKES", shannon, weight=5)
<a name="#cypher"></a>Cypher
If you're returning tabular results, use cypher, which will give you a data.frame.
query = "
MATCH (nicole:Person)-[r:LIKES]->(p:Person)
WHERE nicole.name = 'Nicole'
RETURN nicole.name, r.weight, p.name
"
cypher(graph, query)
## nicole.name r.weight p.name
## 1 Nicole 5 Shannon
## 2 Nicole 1 Kenny
For anything more complicated, use cypherToList, which will give you a list.
query = "
MATCH (nicole:Person)-[:LIKES]->(p:Person)
WHERE nicole.name = 'Nicole'
RETURN nicole, COLLECT(p.name) AS friends
"
cypherToList(graph, query)
## [[1]]
## [[1]]$nicole
## < Node >
## Person
##
## $name
## [1] "Nicole"
##
## $age
## [1] 24
##
##
## [[1]]$friends
## [[1]]$friends[[1]]
## [1] "Shannon"
##
## [[1]]$friends[[2]]
## [1] "Kenny"
Both cypher and cypherToList accept parameters. These parameters can be passed individually or as a list.
query = "
MATCH (p1:Person)-[r:LIKES]->(p2:Person)
WHERE p1.name = {name1} AND p2.name = {name2}
RETURN p1.name, r.weight, p2.name
"
cypher(graph, query, name1="Nicole", name2="Shannon")
## p1.name r.weight p2.name
## 1 Nicole 5 Shannon
cypher(graph, query, list(name1="Nicole", name2="Shannon"))
## p1.name r.weight p2.name
## 1 Nicole 5 Shannon
<a name="#shortest-paths"></a>Shortest Paths
p = shortestPath(greta, "LIKES", shannon, max_depth=4)
n = nodes(p)
sapply(n, "[[", "name")
## [1] "Greta" "Nicole" "Shannon"
<a name="#weighted-shortest-paths"></a>Weighted Shortest Paths
p = shortestPath(greta, "LIKES", shannon, max_depth=4, cost_property="weight")
n = nodes(p)
sapply(n, "[[", "name")
## [1] "Greta" "Nicole" "Kenny" "Shannon"
p$weight
## [1] 11
<a name="#cypher"></a>Graph Algorithms
library(igraph)
query = "
MATCH (n)-->(m)
RETURN n.name, m.name
"
edgelist = cypher(graph, query)
ig = graph.data.frame(edgelist, directed=F)
betweenness(ig)
## Nicole Greta Kenny Shannon
## 2 0 0 0
closeness(ig)
## Nicole Greta Kenny Shannon
## 0.3333333 0.2000000 0.2500000 0.2500000
<a name="#visualizations"></a>Visualizations
igraph
plot(ig)
ggnet
library(network)
library(GGally)
net = network(edgelist)
ggnet(net, label.nodes=TRUE)
visNetwork
Read this blog post and check out this slide deck.
<a name="#import"></a>Import
library(hflights)
hflights = hflights[sample(nrow(hflights), 1000), ]
row.names(hflights) = NULL
head(hflights)
## Year Month DayofMonth DayOfWeek DepTime ArrTime UniqueCarrier FlightNum
## 1 2011 1 15 6 927 1038 XE 2885
## 2 2011 10 10 1 2001 2322 XE 4243
## 3 2011 6 15 3 1853 2108 CO 670
## 4 2011 4 10 7 2100 102 CO 410
## 5 2011 1 25 2 739 1016 XE 3083
## 6 2011 9 13 2 1745 1841 CO 1204
## TailNum ActualElapsedTime AirTime ArrDelay DepDelay Origin Dest Distance
## 1 N34110 131 113 -10 -3 IAH COS 809
## 2 N13970 141 127 2 19 IAH CMH 986
## 3 N36207 255 231 15 -2 IAH SFO 1635
## 4 N76517 182 162 -18 5 IAH EWR 1400
## 5 N12922 157 128 0 -6 IAH MKE 984
## 6 N35271 56 34 -7 -5 IAH SAT 191
## TaxiIn TaxiOut Cancelled CancellationCode Diverted
## 1 6 12 0 0
## 2 4 10 0 0
## 3 5 19 0 0
## 4 7 13 0 0
## 5 4 25 0 0
## 6 3 19 0 0
addConstraint(graph, "Carrier", "name")
addConstraint(graph, "Airport", "name")
query = "
CREATE (flight:Flight {number: {FlightNum} })
SET flight.year = TOINT({Year}),
flight.month = TOINT({DayofMonth}),
flight.day = TOINT({DayOfWeek})
MERGE (carrier:Carrier {name: {UniqueCarrier} })
CREATE (flight)-[:OPERATED_BY]->(carrier)
MERGE (origin:Airport {name: {Origin} })
MERGE (dest:Airport {name: {Dest} })
CREATE (flight)-[o:ORIGIN]->(origin)
CREATE (flight)-[d:DESTINATION]->(dest)
SET o.delay = TOINT({DepDelay}),
o.taxi_time = TOINT({TaxiOut})
SET d.delay = TOINT({ArrDelay}),
d.taxi_time = TOINT({TaxiIn})
"
tx = newTransaction(graph)
for(i in 1:nrow(hflights)) {
row = hflights[i, ]
appendCypher(tx, query,
FlightNum=row$FlightNum,
Year=row$Year,
DayofMonth=row$DayofMonth,
DayOfWeek=row$DayOfWeek,
UniqueCarrier=row$UniqueCarrier,
Origin=row$Origin,
Dest=row$Dest,
DepDelay=row$DepDelay,
TaxiOut=row$TaxiOut,
ArrDelay=row$ArrDelay,
TaxiIn=row$TaxiIn)
}
commit(tx)
summary(graph)
## This To That
## 1 Flight OPERATED_BY Carrier
## 2 Flight ORIGIN Airport
## 3 Flight DESTINATION Airport
<a name="#connection-issues"></a>Connection Issues
Couldn't connect to server
Error in curl::curl_fetch_memory(url, handle = handle) :
Couldn't connect to server
Neo4j probably isn't running. Make sure Neo4j is running first. It's also possible you have localhost resolution issues; try connecting to http://127.0.0.1:7474/db/data/ instead.
No authorization header supplied
Error: client error: (401) Unauthorized
Neo.ClientError.Security.AuthorizationFailed
No authorization header supplied.
You have auth enabled on Neo4j and either didn't provide your username and password or they were invalid. You can pass a username and password to startGraph.
graph = startGraph("http://localhost:7474/db/data/", username="neo4j", password="password")
You can also disable auth by editing the following line in conf/neo4j-server.properties.
# Require (or disable the requirement of) auth to access Neo4j
dbms.security.auth_enabled=false
<a name="#contribute"></a>Contribute
Check out the contributing doc if you'd like to contribute!