Components class for homologous series.

Source: R/components-nontarget.R, R/components-nontarget-set.R

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

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

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

# S4 method for class '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

The name of the set.

...

Further arguments passed to the non-sets workflow method.

Value

plotGraph returns the result of visNetwork.

Details

Objects from this class are generated by generateComponentsNontarget

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

componentsNTSetcomponentsNT

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).

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

Loos2017patRoon

enviPat1

igraph2