Plot the neighborhood of a gene group

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Description

This method plots the neighborhood extracted using getNeighborhood in a visually pleasing way. It is mainly a wrapper around plot.igraph to ensure the proper information is visualised.

Usage

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plotNeighborhood(object, ...)

## S4 method for signature 'pgVirtualLoc'
plotNeighborhood(object, group, vicinity = 4, ...)

Arguments

object

A pgVirtualLoc subclass

...

Parameter passed on to igraph's plot method.

group

The name or index of a group.

vicinity

An integer giving the number of gene groups in both directions to collect.

Value

Called for the side effect of creating a plot. Invisibly returns an igraph object with all visual parameters set as node and edge attributes.

Methods (by class)

  • pgVirtualLoc: Gene group neighborhood plotting for all pgVirtualLoc subclasses

Examples

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testPG <- .loadPgExample(geneLoc=TRUE, withNeighborhoodSplit=TRUE)

# Nice little overview of the neighborhood of gene group 30
plotNeighborhood(testPG, 30)

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