build a graph of EDAM terms deemed relevant to a text — edam_graph • biocEDAM

build a graph of EDAM terms deemed relevant to a text

Usage

edam_graph(txt, edam_graph, provider = "anthropic", ...)

Arguments

txt: string, typically describing a software artifact
edam_graph: an ontologyIndex ontology-index instance representing EDAM
provider: character(1) LLM provider; see llm_env_var. Defaults to "anthropic".
...: passed to ontoProc::onto_plot2

Value

called for its side effect (a graph plot); returns the result of ontoProc::onto_plot2 invisibly

Note

The text is expected to be generated as the 'focused' result of vig2data; it will then be processed by 'edamize'

Examples

if (interactive()) {
requireNamespace("ontoProc2")
eg = readRDS(system.file("rds", "edam_1.25_ontoindex.rds", package="biocEDAM"))
statescoper = readRDS(system.file("rds", "tgac-vumc_StatescopeR.rds", package="biocEDAM"))
edam_graph(statescoper$focused, eg, cex=.3)
}