Get files with modules' graphs

Creates graphical representations of the identified metabolic modules. For each module, the function annotates genes and metabolites, generates network layouts, and exports the results in multiple formats suitable for visualization and downstream analysis. Supported outputs include PDF, PNG, SVG, GraphML, and XGMML files. These visualizations facilitate biological interpretation of the detected metabolic subnetworks.

Usage

getGraphs(
  modules,
  network.annotation,
  metabolites.annotation,
  seed.for.layout = 22,
  work.dir = work.dir
)

Arguments

modules

Metabolic modules.

network.annotation

Metabolic network annotation.

metabolites.annotation

Metabolites annotation.

seed.for.layout

Random seed required for gatom to draw metabolic graph. each atom to corresponding metabolite's name

work.dir

Working directory where results should be saved.

Value

Results of this function can be seen in work.dir (.pdf, .png and .xgmml files).