create_pathway_with_reactions: Creates the pathway, with reactions included in the nodes

In specmine: Metabolomics and Spectral Data Analysis and Mining

Creates the pathway, with reactions included in the nodes

Description

Creates the pathway, with reactions included in the nodes

Usage

create_pathway_with_reactions(
  path,
  path.name,
  identified_cpds,
  nodeNames = "kegg",
  nodeTooltip = FALSE,
  map.zoom = FALSE,
  map.layout = "preset",
  map.width = NULL,
  map.height = NULL
)

Arguments

path	TODO.
path.name	TODO.
identified_cpds	TODO.
nodeNames	TODO.
nodeTooltip	TODO.
map.zoom	TODO.
map.layout	TODO.
map.width	TODO.
map.height	TODO.

Value

A cyjShiny widget representing the pathway with reactions included in the nodes. The widget contains the pathway graph ready for interactive visualization, with identified compounds highlighted when they are present in the pathway.

Examples

## Not run: 
path <- get_MetabolitePath("hsa00010")
create_pathway_with_reactions(
  path = path,
  path.name = "hsa00010",
  identified_cpds = c("cpd:C00031", "cpd:C00022")
)

## End(Not run)

specmine documentation built on Aug. 5, 2026, 5:06 p.m.