generic.Rarefac: Plot and summary of 'Rarefac' objects

Description Usage Arguments Details Author(s) See Also Examples

Description

Generic functions for Rarefac object.

Usage

1
2
3
4
5
6
## S3 method for class 'Rarefac'
plot(x, type = "b", pch = 16, xlab = "Genomes",
  ylab = "Number of unique gene clusters", ...)

## S3 method for class 'Rarefac'
summary(object, ...)

Arguments

x

A Rarefac object, see below.

type

Type of plot, default is "b", giving markers with lines between.

pch

Marker type, default is 16, a filled circle.

xlab

Text for horizontal axis.

ylab

Text for vertical axis.

object

A Rarefac object, see below.

...

Optional graphical arguments.

Details

A Rarefac object is a small (S3) extension to a matrix. The first column contains the cumulative number of unique gene clusters found when considering 1,2,...,G genomes in a pan-matrix. Thus, the Rarefac object is a matrix with G rows. Any additional columns will hold similar numbers, but for random shufflings of the genome's ordering. A Rarefac object is typically created by the function rarefaction.

The plot.Rarefac function will display the content of the Rarefac object as a plot of the mean value in rows 1,2,...,G, where G is the total number of genomes in the study.

The summary.Rarefac function will display a text giving the same information as plot.Rarefac.

Author(s)

Lars Snipen and Kristian Hovde Liland.

See Also

rarefaction, heaps.

Examples

1
# See examples in the Help-file for rarefaction.

micropan documentation built on May 29, 2017, 11:57 a.m.