Base transformation products (TP) class with formula information

Holds information for all TPs for a set of parents, including chemical formulae.

Usage

# S4 method for class 'transformationProductsFormula'
plotGraph(
  obj,
  which,
  components = NULL,
  prune = TRUE,
  onlyCompletePaths = FALSE,
  width = NULL,
  height = NULL
)

Arguments

obj: transformationProductsFormula derived object to be accessed
which: Either a character or integer vector with one or more names/indices of the parents to plot.
components: If specified (i.e. not NULL), a componentsTPs object that is used for matching the graph with screening results. The TPs that were found will be marked. See also the prune and onlyCompletePaths arguments.
prune: If TRUE and components is set, then pathways without any detected TPs are not shown (pruned). See also the onlyCompletePaths and components arguments.
onlyCompletePaths: If TRUE and components is set, then only pathways are shown for which all TPs were detected. See also the prune and components arguments.
width, height: Passed to visNetwork.

Value

plotGraph returns the result of visNetwork.

Details

This (virtual) class is derived from the transformationProducts base class, please see its documentation for more details. Objects from this class are returned by TP generators. More specifically, algorithms that works with chemical formulae (e.g. library_formula), uses this class to store their results. The methods defined for this class extend the functionality for the base transformationProducts class.

Methods (by generic)

plotGraph(transformationProductsFormula): Plots an interactive hierarchy graph of the transformation products. The resulting graph can be browsed interactively and allows exploration of the different TP formation pathways. Furthermore, results from TP componentization can be used to match the hierarchy with screening results. The graph is rendered with visNetwork.

S4 class hierarchy

transformationProducts
- transformationProductsFormula
  - transformationProductsAnnForm
  - transformationProductsLibraryFormula