FindMyFriends (version 1.2.2)

plotEvolution: 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, ...)
"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')