Add resources to graph — addResource • ariadne

addResource includes a user-defined resource to the ariadne graph.

addResource(graph, ...)

# S4 method for class 'igraph'
addResource(graph, file, res.name = "Custom", force = FALSE, ...)

Arguments

graph: An igraph object.
...: Additional arguments passed to fread.
file: Character scalar. The path to a local or remote file that stores the linkmap between two features. It must be a table with two named columns (features) and each row representing a binding between features.
res.name: Character scalar. The name of the resource that will appear in the output graph. (Default: "Custom")
force: Logical scalar. Whether file should overwrite any previously cached files with the same name. (Default: FALSE)

Value

An igraph object.

Examples

# Retrieve resource graph
graph <- ariadne()

# Set URL to custom resource
url <- "https://ftp.ebi.ac.uk/pub/databases/amr_portal/releases/2025-12/"
url <- paste0(url, "genotype.csv.gz")

# Add resource to ariadne graph
graph <- addResource(
    graph,
    url,
    res.name = "AMR",
    select = c("taxon_id", "antibiotic_ontology"),
    col.names = c("taxid", "aro")
)

# Search for newly added path
searchPath(graph, taxid ~ aro)
#> Path 1:
#> taxid -(AMR)-> aro
#> 

# Plot first 5 paths excluding uniref50 and uniref100
plotPath(graph, taxid ~ aro, focus = TRUE)
#> Warning: Using alpha for a discrete variable is not advised.


# Find antibiotics related to E. coli (NCBI 562)
tax2aro <- weavePath(graph, taxid ~ aro, init = 562)
#> taxid -(AMR)-> aro