componentsNT-class: Components class for homologous series.

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

Components class for homologous series.

Description

This class is derived from components and is used to store results from unsupervised homolog detection with the nontarget package.

Usage

## S4 method for signature 'componentsNT'
plotGraph(obj, onlyLinked = TRUE, width = NULL, height = NULL)

## S4 method for signature 'componentsNTSet'
plotGraph(obj, onlyLinked = TRUE, set, ...)

## S4 method for signature 'componentsNTSet'
unset(obj, set)

Arguments

obj	The componentsNT object to plot.
onlyLinked	If TRUE then only components with links are plotted.
width, height	Passed to visNetwork.
set	\setsWF The name of the set.
...	\setsWF Further arguments passed to the non-sets workflow method.

Details

Objects from this class are generated by generateComponentsNontarget

Value

plotGraph returns the result of visNetwork.

Methods (by generic)

• plotGraph(componentsNT): Plots an interactive network graph for linked homologous series (i.e. series with (partial) overlap which could not be merged). The resulting graph can be browsed interactively and allows quick inspection of series which may be related. The graph is constructed with the igraph package and rendered with visNetwork.

Slots

homol

A list with homol objects for each replicate group as returned by homol.search

Sets workflows

\setsWFClass

componentsNTSetcomponentsNT

\setsWFNewMethodsSO

componentsNTUnsetOnly the components in the specified set are kept. Furthermore, the component names are restored to non-set specific names (see generateComponents for more details).

\setsWFChangedMethods \item

plotGraph Currently can only create graph networks from one set (specified by the set argument).

Note that the componentsNTSet class does not have a homol slot. Instead, the setObjects method can be used to access this data for a specific set.

References

\insertRef

Loos2017patRoon

\addCitationsenviPat1

\addCitations

igraph2

See Also

components and generateComponents

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