Plotting and printing Rarefac objects

Description

Generic functions for plotting and printing the content of a Rarefac object.

Usage

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

Arguments

x

A Rarefac object, see below.

object

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.

...

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.

The str.Rarefac function will simply print the number of genomes of the Rarefac object.

Author(s)

Lars Snipen and Kristian Hovde Liland.

See Also

rarefaction, heaps.

Examples

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# Loading a Panmat objects in the micropan package
data(list="Mpneumoniae.blast.panmat",package="micropan")

# Computing Rarefaction
rarefac.blast <- rarefaction(Mpneumoniae.blast.panmat,n.perm=100)


# Plotting and printing the Rarefac object
plot(rarefac.blast)
summary(rarefac.blast)
str(rarefac.blast)

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