plotNeighborhood: Plot the neighborhood of a gene group

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

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

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

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

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

thomasp85/FindMyFriends documentation built on April 25, 2020, 1:06 p.m.