plotGroup {FindMyFriends} | R Documentation

## Plot the similarities of genes within a group

### Description

This method plots a gene group with genes as vertices and cosine similarities as weighted edges. Mildly informative at best :-)

### Usage

    plotGroup(object, ...)

    ## S4 method for signature 'pgVirtual'
    plotGroup(object, group, kmerSize, lowerLimit,
      rescale, transform, ...)

### Arguments

`object` | A pgVirtual subclass
`...` | Parameters to be passed on to igraphs plotting method
`group` | Name or index of the gene group to plot
`kmerSize` | The kmer size to use for similarity calculations
`lowerLimit` | The lower threshold for similarity below which it will be set to 0
`rescale` | logical. Should the similarity be rescaled between lowerLimit and 1
`transform` | A transformation function to apply to the similarities

### 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)

- `pgVirtual`: Gene group similiarity plotting for all pgVirtual subclasses

### Examples

    testPG <- .loadPgExample(withGroups=TRUE)

    plotGroup(testPG, 10, lowerLimit=0.25)

[Package FindMyFriends version 1.16.0 Index]