transformationProductsFormula-class: Base transformation products (TP) class with formula...

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Base transformation products (TP) class with formula information

Description

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

Usage

## S4 method for signature '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.

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.

Value

plotGraph returns the result of visNetwork.

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

    • transformationProductsLibraryFormula

See Also

The base class transformationProducts for more relevant methods and generateTPs

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.