plotEvolution {FindMyFriends} | R Documentation

## Plot the evolution in gene groups

### Description

This method constructs a plot showing how the number of singleton, accessory and core gene groups evolve as the size of the pangenome increases. Different ways of increasing the size of the pangenome is available.

### Usage

    plotEvolution(object, ...)

    ## S4 method for signature 'pgVirtual'
    plotEvolution(object, ordering = "bootstrap",
      times = 10)

### Arguments

`object` | A pgVirtual subclass
`...` | Parameters to be passed on
`ordering` | An ordering of the organisms by name or index, or alternative one of 'bootstrap', 'random' or 'none'.
`times` | The number of sampling for ordering='bootstrap'

### Value

This function is called for its side effects

### Methods (by class)

- `pgVirtual`: Evolution plots for pgVirtual subclasses

### Examples

    testPG <- .loadPgExample(withGroups=TRUE)

    # Standard type - organisms ordered by their index in the pangenome
    plotEvolution(testPG, ordering='none')

    # Bootstrapped with confidence intervals
    plotEvolution(testPG, ordering='bootstrap')

[Package FindMyFriends version 1.17.0 Index]