plotNeighborhood {FindMyFriends} | R Documentation

## Plot the neighborhood of a gene group

### 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)

[Package FindMyFriends version 1.14.0 Index]