micropan (version 1.2)

plot.Panmat: Plot and summary of Panmat objects

Description

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

Usage

# S3 method for Panmat
plot(x, col = "black", xlab = "Number of genomes",
  ylab = "Number of clusters", ...)
# S3 method for Panmat
summary(object, ...)

Arguments

x

A Panmat object, see below.

col

The color, default is "black", of interior and borders of the bars in the barplot.

xlab

The label of the X axis.

ylab

The label of the Y axis.

…

Optional (graphical) arguments.

object

A Panmat object, see below.

Details

A Panmat object contains a pan-matrix, which is the fundamental data structure for pan-genome analyses. It is a small (S3) extension to a matrix. It has one row for each genome in the study, and one column for each gene cluster. The number in cell [i,j] is the number of sequences in genome i that belongs to cluster j. A Panmat object is typically created by the function panMatrix.

The plot.Panmat function will display the content of the Panmat object as a bar chart showing the number of clusters found in 1,2,...,G genomes, where G is the total number of genomes in the study (rows in Panmat).

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

See Also

panMatrix.

Examples

# NOT RUN {
# See examples in the Help-file for panMatrix.

# }