ReactomeGraph4R: an R interface for the Reactome Graph Database
Local Reactome Graph Database setup
- Get Docker: https://docs.docker.com/get-docker
- Download and install the current Reactome Graph Database:
mkdir -p $(pwd)/neo4j/data/databases
download the db file
wget https://reactome.org/download/current/reactome.graphdb.tgz -P $(pwd)/neo4j/data/databases
extract
tar -zxvf $(pwd)/neo4j/data/databases/reactome.graphdb.tgz -C $(pwd)/neo4j/data/databases
run on docker
docker run --name reactome_graph_db -p 7687:7687 -p 7474:7474 -e NEO4J_dbms_allow__upgrade=true -e NEO4J_AUTH=none -v $(pwd)/neo4j/data:/data neo4j:3.5.19
For re-downloading a new release file, remember to remove (`docker rm`) the old container if using the same container name, and do note the owner and group of the directories. You can also list all containers by `docker ps -a`.
3. Launch Neo4j through browser:If you want to set a password, you can remove `NEO4J_AUTH=none` in the `docker run` command. The default username and password are both `neo4j`, after login you will be prompted to change the new password.
Try to explore the Graph Database and query data using Cypher, e.g. getting the database version:MATCH (dbi:DBInfo) RETURN dbi.version
More details see this [tutorial](https://reactome.org/dev/graph-database/extract-participating-molecules).
The next time you run the Graph Database, you can just start running docker and execute:docker start reactome_graph_db
## Installationfrom Bioconductor (BioC >= 3.13)
if (!requireNamespace("BiocManager")) { install.packages("BiocManager") } BiocManager::install("ReactomeGraph4R")
or from GitHub:
devtools::install_github("reactome/ReactomeGraph4R")
## Examples
Read the complementary [__vignette__](https://bioconductor.org/packages/release/bioc/vignettes/ReactomeGraph4R/inst/doc/Introduction.html).
### Loading and connecting
Load the packagelibrary(ReactomeGraph4R) login()
The `login()` is a _required_ step that allows you to connect to your local Neo4j server, by answering two questions:
- Is the url 'http://localhost:7474'? (Yes/no/cancel)
- Does Neo4J require authentication? (Yes/no/cancel)
Results are in these two formats:
- "row": a list of results in dataframes (default)
- "graph": a graph object with nodes and relationships information
### Row data
Using Reactome id:
``` r
matchPrecedingAndFollowingEvents(event.id = "R-HSA-8983688", type = "row")
#> Retrieving immediately connected instances... Specify depth-related arguments for more depths
#> $precedingEvent
#> schemaClass speciesName isInDisease releaseDate displayName stIdVersion dbId name isChimeric stId
#> 1 Reaction Homo sapiens FALSE 2018-09-12 OAS1 binds viral dsRNA R-HSA-8983671.1 8983671 OAS1 binds viral dsRNA FALSE R-HSA-8983671
#> category isInferred
#> 1 binding FALSE
#>
#> $event
#> schemaClass speciesName isInDisease releaseDate displayName stIdVersion dbId name isChimeric stId category
#> 1 Reaction Homo sapiens FALSE 2018-09-12 OAS1 oligomerizes R-HSA-8983688.1 8983688 OAS1 oligomerizes FALSE R-HSA-8983688 binding
#> isInferred
#> 1 FALSE
#>
#> $followingEvent
#> schemaClass speciesName isInDisease releaseDate displayName stIdVersion dbId name isChimeric
#> 1 Polymerisation Homo sapiens FALSE 2018-09-12 OAS1 produces oligoadenylates R-HSA-8983680.1 8983680 OAS1 produces oligoadenylates FALSE
#> stId category isInferred
#> 1 R-HSA-8983680 transition FALSE
#>
#> $relationships
#> neo4jId type startNode.neo4jId startNode.dbId startNode.schemaClass endNode.neo4jId endNode.dbId endNode.schemaClass properties
#> 1 7685968 precedingEvent 1808570 8983680 Polymerisation 1808457 8983688 Reaction 1, 0
#> 2 7685746 precedingEvent 1808457 8983688 Reaction 1808512 8983671 Reaction 1, 0Using non-Reactome id:
row <- matchHierarchy(id = "P33992", databaseName = "UniProt", type = "row")
str(row, max.level = 1)
#> List of 5
#> $ referenceEntity:'data.frame': 1 obs. of 17 variables:
#> $ physicalEntity :'data.frame': 1 obs. of 12 variables:
#> $ event :'data.frame': 1 obs. of 12 variables:
#> $ upperevent :'data.frame': 6 obs. of 18 variables:
#> $ relationships :'data.frame': 8 obs. of 9 variables:row looks like the returned result of the last command.
Graph data
Every graph result contains two dataframes - "nodes" and "relationships".
graph <- matchHierarchy(id = "P33992", databaseName = "UniProt", type = "graph")
str(graph, max.level = 2)
#> List of 2
#> $ nodes :'data.frame': 9 obs. of 3 variables:
#> ..$ id : chr [1:9] "422883" "90375" "422833" "90376" ...
#> ..$ label :List of 9
#> ..$ properties:List of 9
#> $ relationships:'data.frame': 8 obs. of 5 variables:
#> ..$ id : chr [1:8] "1700863" "1701159" "360682" "1813950" ...
#> ..$ type : chr [1:8] "output" "hasEvent" "referenceEntity" "hasEvent" ...
#> ..$ startNode : chr [1:8] "422833" "422883" "90375" "449402" ...
#> ..$ endNode : chr [1:8] "90375" "422833" "90376" "422883" ...
#> ..$ properties:List of 8graph could then be converted to objects in network visualization packages. The following is an example to get a visNetwork object from graph.
Extract nodes and edges from our result:
relationships <- graph[["relationships"]]
nodes <- graph[["nodes"]]
nodes <- unnestListCol(df = nodes, column = "properties")Then select some columns:
library(stringr)
vis.nodes <- data.frame(id = nodes$id,
label = str_trunc(nodes$displayName, 20),
group = nodes$schemaClass,
title = paste0("<p><b>", nodes$schemaClass, "</b><br>",
"dbId: ", nodes$dbId, "<br>", nodes$displayName, "</p>"))
vis.edges <- data.frame(from = relationships$startNode,
to = relationships$endNode,
label = relationships$type,
font.size = 16,
font.color = 'steelblue')Add parameters for nodes:
library(wesanderson) # for color palette
node.colors <- as.character(wes_palette(n = length(unique(vis.nodes$group)), name = "Darjeeling2"))
names(node.colors) <- levels(factor(vis.nodes$group))
vis.nodes$color.background <- node.colors[as.numeric(factor(vis.nodes$group))]
vis.nodes$color.border <- "lightgray"
vis.nodes$color.border[vis.nodes$label == "UniProt:P33992 MCM5"] <- "pink"
vis.nodes$color.highlight.border <- "darkred"
vis.nodes$borderWidth <- 2 # Node border widthAdd parameters for edges:
vis.edges$width <- 1.2
edges.colors <- as.character(wes_palette(n = length(unique(vis.edges$label)), name = "FantasticFox1"))
names(edges.colors) <- unique(vis.edges$label)
vis.edges$color <- str_replace_all(vis.edges$label, edges.colors)
vis.edges$arrows <- "to"
vis.edges$smooth <- TRUE
library(visNetwork)
visNetwork(vis.nodes, vis.edges, main = "The hierarchy of protein MCM5",
height = "500px", width = "100%")
Find the interactive graphs in the vignette!
Feedback
We'd love to hear your feedback! Feel free to contribute any new features and/or open an issue on GitHub.