get_graph: Get igraph object

In vanhasseltlab/IMatlas: a tool for design and interpretation of metabolomics studies in immunology

Get igraph object

Description

Get igraph object

Usage

get_graph(
   filter,
   neighbours = 0,
   max_neighbours = Inf,
   simple = F,
   omit_lipids = F,
   type = "Immune process by name",
   search_mode = "Interacts",
   verbose = T
)

Arguments

filter	String containing the search term.
neighbours	Integer containing the number of neighbours to be found
max_neighbours	Integer representing the maximum number of edges for each neighbour
simple	Boolean value indicating to return a barebone graph or including metadata.
omit_lipids	Boolean value if lipids should be omitted
type	String containing the type of search.
search_mode	String of either 'Interacts' or 'Between'. Interacts finds the first neighbour of the given search, while Between only returns interactions between the proteins / metabolites given.
verbose	Boolean value, should info be printed?

Examples

# Construct a GO graph
## Not run: 
g <- get_graph("microglial cell activation")
g <- get_graph("microglial cell activation", 0, "Gene Ontology")
# Construct a graph using Metabolites and/or Proteins
g <- get_graph("L-Asparagine", type = "Metabolites/Proteins")

## End(Not run)

vanhasseltlab/IMatlas documentation built on Jan. 31, 2023, 12:27 a.m.