pathway_analysis: Creates the pathway wanted. If any of the given compounds is...

In specmine: Metabolomics and Spectral Data Analysis and Mining

Creates the pathway wanted. If any of the given compounds is present in the pathway, it is coloured differently.

Description

Creates the pathway wanted. If any of the given compounds is present in the pathway, it is coloured differently.

Usage

pathway_analysis(
  compounds,
  pathway,
  nodeNames = "kegg",
  nodeTooltip = FALSE,
  map.zoom = FALSE,
  map.layout = "preset",
  map.width = NULL,
  map.height = NULL,
  verbose = TRUE
)

Arguments

compounds	TODO.
pathway	TODO.
nodeNames	TODO.
nodeTooltip	TODO.
map.zoom	TODO.
map.layout	TODO.
map.width	TODO.
map.height	TODO.
verbose	Logical indicating whether progress messages should be shown.

Value

A cyjShiny widget representing the selected pathway with the input compounds highlighted when present. The returned widget can be printed or embedded in an interactive R session to inspect the pathway graph.

Examples

## Not run: 
pathway_analysis(
  compounds = c(glucose = "cpd:C00031", pyruvate = "cpd:C00022"),
  pathway = "hsa00010",
  verbose = FALSE
)

## End(Not run)

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