plotEvolution: Plot the evolution in gene groups

In FindMyFriends: Microbial Comparative Genomics in R

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')

FindMyFriends documentation built on Nov. 8, 2020, 6:46 p.m.